rs2682406

Positions:

• chr3-158308700-T-A
• chr3-158308700-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001271838.2(RSRC1):​c.531+10625T>A variant causes a intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,714 control chromosomes in the GnomAD database, including 18,236 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 0.48 (18236 hom., cov: 32)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.54

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.531+10625T>A		intron_variant		ENST00000611884.5	NP_001258767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSRC1	ENST00000611884.5	c.531+10625T>A		intron_variant		5	NM_001271838.2	ENSP00000481697	P4

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73016 AN: 151596 Hom.: 18214 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.482 AC: 73085 AN: 151714 Hom.: 18236 Cov.: 32 AF XY: 0.484 AC XY: 35863 AN XY: 74148

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.496

Alfa AF: 0.454 Hom.: 1986

Bravo AF: 0.485

Asia WGS AF: 0.444 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	22
DANN	Benign	0.89

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: rs2682406; hg19: chr3-158026489;