rs11130146

Positions:

• chr3-47666322-C-A

Variant summary

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

The NM_003074.4(SMARCC1):​c.1900-3730G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,026 control chromosomes in the GnomAD database, including 28,194 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 0.60 (28194 hom., cov: 31)
• Consequence: SMARCC1 NM_003074.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

Genes affected

SMARCC1 (HGNC:11104): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c 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 contains a predicted leucine zipper motif typical of many transcription factors. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMARCC1	NM_003074.4	c.1900-3730G>T		intron_variant		ENST00000254480.10	NP_003065.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMARCC1	ENST00000254480.10	c.1900-3730G>T		intron_variant		1	NM_003074.4	ENSP00000254480	P1
SMARCC1	ENST00000425518.5	n.1790-3730G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90461 AN: 151908 Hom.: 28193 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.594

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.595 AC: 90497 AN: 152026 Hom.: 28194 Cov.: 31 AF XY: 0.600 AC XY: 44586 AN XY: 74292

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.587

Alfa AF: 0.638 Hom.: 14293

Bravo AF: 0.576

Asia WGS AF: 0.582 AC: 2026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.46

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: rs11130146; hg19: chr3-47707812;