12-50086481-G-GGTGGTGGTA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003076.5(SMARCD1):c.366-132_366-131insAGTGGTGGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00973 in 955,222 control chromosomes in the GnomAD database, including 536 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.036 (343 hom., cov: 33)
  • Exomes 𝑓: 0.0048 (193 hom.)
• Consequence: SMARCD1 NM_003076.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.21

Genes affected

SMARCD1 (HGNC:11106): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1) The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which 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 and has sequence similarity to the yeast Swp73 protein. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 12-50086481-G-GGTGGTGGTA is Benign according to our data. Variant chr12-50086481-G-GGTGGTGGTA is described in ClinVar as [Benign]. Clinvar id is 1245538.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMARCD1	NM_003076.5	c.366-132_366-131insAGTGGTGGT		intron_variant		ENST00000394963.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMARCD1	ENST00000394963.9	c.366-132_366-131insAGTGGTGGT		intron_variant		1	NM_003076.5	P1

Frequencies

GnomAD3 genomes AF: 0.0357 AC: 5408 AN: 151376 Hom.: 336 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0170

Gnomad ASJ AF: 0.000868

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000324

Gnomad OTH AF: 0.0276

GnomAD4 exome AF: 0.00480 AC: 3855 AN: 803728 Hom.: 193 Cov.: 13 AF XY: 0.00403 AC XY: 1661 AN XY: 412154

Gnomad4 AFR exome AF: 0.130

Gnomad4 AMR exome AF: 0.00812

Gnomad4 ASJ exome AF: 0.000463

Gnomad4 EAS exome AF: 0.0000607

Gnomad4 SAS exome AF: 0.000722

Gnomad4 FIN exome AF: 0.000121

Gnomad4 NFE exome AF: 0.00123

Gnomad4 OTH exome AF: 0.0108

GnomAD4 genome AF: 0.0359 AC: 5439 AN: 151494 Hom.: 343 Cov.: 33 AF XY: 0.0348 AC XY: 2579 AN XY: 74028

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.000868

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000324

Gnomad4 OTH AF: 0.0274

Alfa AF: 0.0218 Hom.: 0

Asia WGS AF: 0.0110 AC: 39 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 01, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555186252; hg19: chr12-50480264;