rs61761957

Variant names:

• chr19-11033406-G-A
• rs61761957
• NM_001387283.1:c.3663G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-11033406-G-A
• chr19-11033406-G-C
• chr19-11033406-G-T

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BS1 BS2

The NM_001387283.1(SMARCA4):​c.3663G>A​(p.Lys1221Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000276 in 1,613,498 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0015 (3 hom., cov: 33)
  • Exomes 𝑓: 0.00015 (2 hom.)
• Consequence: SMARCA4 NM_001387283.1 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7
• Conservation: PhyloP100: 1.03
• Publications: 1 publications found

Genes affected

SMARCA4 (HGNC:11100): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4) The protein encoded by this gene is a member of the SWI/SNF family of proteins and is similar to the brahma protein of Drosophila. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. In addition, this protein can bind BRCA1, as well as regulate the expression of the tumorigenic protein CD44. Mutations in this gene cause rhabdoid tumor predisposition syndrome type 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

SMARCA4 Gene-Disease associations (from GenCC):

• Coffin-Siris syndrome

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet, Illumina
• intellectual disability, autosomal dominant 16

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• rhabdoid tumor predisposition syndrome 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, ClinGen, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), G2P
• uterine corpus sarcoma

  Inheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
• familial rhabdoid tumor

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary nonpolyposis colon cancer

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BP6: Variant 19-11033406-G-A is Benign according to our data. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11033406-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 238432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=1.03 with no splicing effect.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00146 (223/152294) while in subpopulation AFR AF = 0.00517 (215/41560). AF 95% confidence interval is 0.00461. There are 3 homozygotes in GnomAd4. There are 110 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 3 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.3663G>A	p.Lys1221Lys	synonymous_variant	Exon 26 of 36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.3663G>A	p.Lys1221Lys	synonymous_variant	Exon 26 of 35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.3663G>A	p.Lys1221Lys	synonymous_variant	Exon 26 of 36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.3663G>A	p.Lys1221Lys	synonymous_variant	Exon 26 of 35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.3663G>A	p.Lys1221Lys	synonymous_variant	Exon 26 of 35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.3663G>A	p.Lys1221Lys	synonymous_variant	Exon 27 of 35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.3663G>A	p.Lys1221Lys	synonymous_variant	Exon 26 of 34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.3663G>A	p.Lys1221Lys	synonymous_variant	Exon 26 of 34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.3663G>A	p.Lys1221Lys	synonymous_variant	Exon 27 of 35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.3075G>A	p.Lys1025Lys	synonymous_variant	Exon 23 of 32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.2307G>A	p.Lys769Lys	synonymous_variant	Exon 19 of 28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.2388G>A	p.Lys796Lys	synonymous_variant	Exon 19 of 27			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.2148G>A	p.Lys716Lys	synonymous_variant	Exon 18 of 27			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.2016G>A	p.Lys672Lys	synonymous_variant	Exon 17 of 25			ENSP00000494159.1
SMARCA4	ENST00000538456.4	c.-82G>A		upstream_gene_variant		3		ENSP00000495197.1

Frequencies

GnomAD3 genomes AF: 0.00146 AC: 222 AN: 152176 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.00516

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000262

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00191

GnomAD2 exomes AF: 0.000418 AC: 105 AN: 251218 AF XY: 0.000272

Gnomad AFR exome AF: 0.00591

Gnomad AMR exome AF: 0.000202

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000881

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000153 AC: 223 AN: 1461204 Hom.: 2 Cov.: 32 AF XY: 0.000116 AC XY: 84 AN XY: 726906

African (AFR) AF: 0.00565 AC: 189 AN: 33480

American (AMR) AF: 0.000246 AC: 11 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.0000116 AC: 1 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52754

Middle Eastern (MID) AF: 0.000520 AC: 3 AN: 5768

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1111996

Other (OTH) AF: 0.000282 AC: 17 AN: 60388

GnomAD4 genome AF: 0.00146 AC: 223 AN: 152294 Hom.: 3 Cov.: 33 AF XY: 0.00148 AC XY: 110 AN XY: 74462

African (AFR) AF: 0.00517 AC: 215 AN: 41560

American (AMR) AF: 0.000262 AC: 4 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68012

Other (OTH) AF: 0.00189 AC: 4 AN: 2116

Alfa AF: 0.000752 Hom.: 2

Bravo AF: 0.00165

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary cancer-predisposing syndrome Benign:2

Mar 26, 2021

Sema4, Sema4

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: curation

- -

May 26, 2015

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

not specified Benign:1

Jun 15, 2017

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Intellectual disability, autosomal dominant 16 Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Rhabdoid tumor predisposition syndrome 2 Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:1

Apr 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SMARCA4: BP4, BP7 -

SMARCA4-related disorder Benign:1

Feb 21, 2020

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	9.6
DANN	Benign	0.59
PhyloP100		1.0
PromoterAI		-0.039	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=95/5	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs61761957; hg19: chr19-11144082;