3-158476931-G-A

Variant names:

• chr3-158476931-G-A
• rs11714869
• NM_001271838.2:c.652+15928G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-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 rank	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.652+15928G>A		intron_variant	Intron 7 of 9	ENST00000611884.5	NP_001258767.1
RSRC1	NM_016625.4	c.652+15928G>A		intron_variant	Intron 7 of 9		NP_057709.2
RSRC1	NM_001271834.2	c.478+15928G>A		intron_variant	Intron 6 of 8		NP_001258763.1
RSRC1	XM_047448275.1	c.652+15928G>A		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.652+15928G>A		intron_variant	Intron 7 of 9	5	NM_001271838.2	ENSP00000481697.1

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

African (AFR) AF: 0.641 AC: 26542 AN: 41434

American (AMR) AF: 0.511 AC: 7797 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1483 AN: 3470

East Asian (EAS) AF: 0.325 AC: 1677 AN: 5156

South Asian (SAS) AF: 0.605 AC: 2917 AN: 4822

European-Finnish (FIN) AF: 0.427 AC: 4503 AN: 10558

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32563 AN: 67934

Other (OTH) AF: 0.495 AC: 1043 AN: 2106

Alfa AF: 0.505 Hom.: 3370

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
PhyloP100		-0.57
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: rs11714869; hg19: chr3-158194720;