rs2584622

chr17-63832807-G-Achr17-63832807-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001098426.2(SMARCD2):c.*131C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.941 in 770,020 control chromosomes in the GnomAD database, including 340,880 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.95 (68548 hom., cov: 32)
  • Exomes 𝑓: 0.94 (272332 hom.)
• Consequence: SMARCD2 NM_001098426.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

Genes affected

SMARCD2 (HGNC:11107): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2) 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. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMARCD2	NM_001098426.2	c.*131C>T		3_prime_UTR_variant	13/13	ENST00000448276.7
SMARCD2	NM_001330439.1	c.*131C>T		3_prime_UTR_variant	13/13
SMARCD2	NM_001330440.2	c.*131C>T		3_prime_UTR_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMARCD2	ENST00000448276.7	c.*131C>T		3_prime_UTR_variant	13/13	1	NM_001098426.2	P1

Frequencies

GnomAD3 genomes AF: 0.949 AC: 144322 AN: 152156 Hom.: 68487 Cov.: 32

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.947

GnomAD4 exome AF: 0.939 AC: 579821 AN: 617746 Hom.: 272332 Cov.: 8 AF XY: 0.939 AC XY: 304656 AN XY: 324286

Gnomad4 AFR exome AF: 0.982

Gnomad4 AMR exome AF: 0.964

Gnomad4 ASJ exome AF: 0.934

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.974

Gnomad4 FIN exome AF: 0.942

Gnomad4 NFE exome AF: 0.924

Gnomad4 OTH exome AF: 0.934

GnomAD4 genome AF: 0.949 AC: 144442 AN: 152274 Hom.: 68548 Cov.: 32 AF XY: 0.952 AC XY: 70834 AN XY: 74444

Gnomad4 AFR AF: 0.983

Gnomad4 AMR AF: 0.953

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.980

Gnomad4 FIN AF: 0.941

Gnomad4 NFE AF: 0.922

Gnomad4 OTH AF: 0.947

Alfa AF: 0.936 Hom.: 31186

Bravo AF: 0.950

Asia WGS AF: 0.989 AC: 3440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	12
Dann	Benign	0.62

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

Publications

LitVar

Other links and lift over

dbSNP: rs2584622; hg19: chr17-61910167;