rs2117764

Variant names:

• chr3-158519071-A-G
• rs2117764
• NM_001271838.2:c.653-18021A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-158519071-A-G
• chr3-158519071-A-T

Variant summary

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

The NM_001271838.2(RSRC1):​c.653-18021A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,960 control chromosomes in the GnomAD database, including 7,424 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 0.31 (7424 hom., cov: 31)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.682
• Publications: 12 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.653-18021A>G		intron_variant	Intron 7 of 9	ENST00000611884.5	NP_001258767.1
RSRC1	NM_016625.4	c.653-18021A>G		intron_variant	Intron 7 of 9		NP_057709.2
RSRC1	NM_001271834.2	c.479-18021A>G		intron_variant	Intron 6 of 8		NP_001258763.1
RSRC1	XM_047448275.1	c.653-18021A>G		intron_variant	Intron 7 of 9		XP_047304231.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSRC1	ENST00000611884.5	c.653-18021A>G		intron_variant	Intron 7 of 9	5	NM_001271838.2	ENSP00000481697.1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46893 AN: 151842 Hom.: 7425 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.309 AC: 46910 AN: 151960 Hom.: 7424 Cov.: 31 AF XY: 0.311 AC XY: 23118 AN XY: 74250

African (AFR) AF: 0.252 AC: 10448 AN: 41486

American (AMR) AF: 0.316 AC: 4830 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1433 AN: 5148

South Asian (SAS) AF: 0.408 AC: 1960 AN: 4806

European-Finnish (FIN) AF: 0.336 AC: 3539 AN: 10542

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.336 AC: 22856 AN: 67940

Other (OTH) AF: 0.301 AC: 634 AN: 2108

Alfa AF: 0.325 Hom.: 26103

Bravo AF: 0.302

Asia WGS AF: 0.359 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.74
PhyloP100		0.68
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: rs2117764; hg19: chr3-158236860;