rs1915935

Variant names:

• chr3-158186611-A-G
• rs1915935
• NM_001271838.2:c.321-16461A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-158186611-A-G
• chr3-158186611-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001271838.2(RSRC1):​c.321-16461A>G variant causes a intron change. The variant allele was found at a frequency of 0.656 in 151,732 control chromosomes in the GnomAD database, including 32,919 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 0.66 (32919 hom., cov: 31)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.22
• Publications: 6 publications found

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]

RSRC1 Gene-Disease associations (from GenCC):

• intellectual developmental disorder, autosomal recessive 70

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
• autosomal recessive non-syndromic intellectual disability

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.321-16461A>G		intron_variant	Intron 3 of 9	ENST00000611884.5	NP_001258767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSRC1	ENST00000611884.5	c.321-16461A>G		intron_variant	Intron 3 of 9	5	NM_001271838.2	ENSP00000481697.1

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99509 AN: 151614 Hom.: 32888 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.656 AC: 99586 AN: 151732 Hom.: 32919 Cov.: 31 AF XY: 0.660 AC XY: 48934 AN XY: 74168

African (AFR) AF: 0.636 AC: 26350 AN: 41420

American (AMR) AF: 0.690 AC: 10496 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2599 AN: 3470

East Asian (EAS) AF: 0.842 AC: 4348 AN: 5164

South Asian (SAS) AF: 0.604 AC: 2916 AN: 4824

European-Finnish (FIN) AF: 0.685 AC: 7241 AN: 10576

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43283 AN: 67758

Other (OTH) AF: 0.684 AC: 1444 AN: 2110

Alfa AF: 0.648 Hom.: 4809

Bravo AF: 0.660

Asia WGS AF: 0.730 AC: 2539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	20
DANN	Benign	0.86
PhyloP100		4.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1915935; hg19: chr3-157904400;