3-158476931-G-A

Position:

• chr3-158476931-G-A

Variant summary

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

The NM_001271838.2(RSRC1):​c.652+15928G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,932 control chromosomes in the GnomAD database, including 21,115 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 0.52 (21115 hom., cov: 32)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

Genes affected

RSRC1 (HGNC:24152): (arginine and serine rich coiled-coil 1) This gene encodes a member of the serine and arginine rich-related protein family. The encoded protein is involved in both constitutive and alternative mRNA splicing. This gene may be associated with schizophrenia. A pseudogene of this gene is located on chromosome 9. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSRC1	NM_001271838.2	c.652+15928G>A		intron_variant		ENST00000611884.5
RSRC1	NM_001271834.2	c.478+15928G>A		intron_variant
RSRC1	NM_016625.4	c.652+15928G>A		intron_variant
RSRC1	XM_047448275.1	c.652+15928G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSRC1	ENST00000611884.5	c.652+15928G>A		intron_variant		5	NM_001271838.2	P4

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78967 AN: 151814 Hom.: 21093 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.520 AC: 79036 AN: 151932 Hom.: 21115 Cov.: 32 AF XY: 0.520 AC XY: 38647 AN XY: 74250

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.495

Alfa AF: 0.501 Hom.: 3216

Bravo AF: 0.529

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.31

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: rs11714869; hg19: chr3-158194720;