3-47611149-C-T

Position:

• chr3-47611149-C-T

Variant summary

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

The NM_003074.4(SMARCC1):​c.2782-822G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,060 control chromosomes in the GnomAD database, including 26,570 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 0.58 (26570 hom., cov: 33)
• Consequence: SMARCC1 NM_003074.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

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]

LOC124906234 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMARCC1	NM_003074.4	c.2782-822G>A		intron_variant		ENST00000254480.10
LOC124906234	XR_007095902.1	n.127-3151C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMARCC1	ENST00000254480.10	c.2782-822G>A		intron_variant		1	NM_003074.4	P1
SMARCC1	ENST00000425518.5	n.2672-822G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87630 AN: 151942 Hom.: 26570 Cov.: 33

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.576 AC: 87654 AN: 152060 Hom.: 26570 Cov.: 33 AF XY: 0.578 AC XY: 42961 AN XY: 74330

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.571

Alfa AF: 0.634 Hom.: 30004

Bravo AF: 0.547

Asia WGS AF: 0.544 AC: 1894 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.38

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: rs1014228; hg19: chr3-47652639;