rs2362965

Variant names:

• chr3-158391590-T-A
• rs2362965
• NM_001271838.2:c.583+36682T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-158391590-T-A
• chr3-158391590-T-C
• chr3-158391590-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001271838.2(RSRC1):​c.583+36682T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,000 control chromosomes in the GnomAD database, including 14,832 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 0.43 (14832 hom., cov: 32)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 19 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.583+36682T>A		intron_variant	Intron 6 of 9	ENST00000611884.5	NP_001258767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSRC1	ENST00000611884.5	c.583+36682T>A		intron_variant	Intron 6 of 9	5	NM_001271838.2	ENSP00000481697.1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65018 AN: 151882 Hom.: 14833 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.428 AC: 65037 AN: 152000 Hom.: 14832 Cov.: 32 AF XY: 0.428 AC XY: 31816 AN XY: 74316

African (AFR) AF: 0.278 AC: 11530 AN: 41498

American (AMR) AF: 0.493 AC: 7531 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1640 AN: 3466

East Asian (EAS) AF: 0.357 AC: 1851 AN: 5178

South Asian (SAS) AF: 0.603 AC: 2905 AN: 4818

European-Finnish (FIN) AF: 0.386 AC: 4081 AN: 10564

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34168 AN: 67892

Other (OTH) AF: 0.429 AC: 907 AN: 2112

Alfa AF: 0.317 Hom.: 852

Bravo AF: 0.426

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.5
DANN	Benign	0.67
PhyloP100		1.2
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: rs2362965; hg19: chr3-158109379;