3-158204321-A-G

Variant names:

• chr3-158204321-A-G
• rs1624094
• NM_001271838.2:c.494+1076A>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.494+1076A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,910 control chromosomes in the GnomAD database, including 25,219 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 0.57 (25219 hom., cov: 32)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.494+1076A>G		intron_variant	Intron 4 of 9	ENST00000611884.5	NP_001258767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSRC1	ENST00000611884.5	c.494+1076A>G		intron_variant	Intron 4 of 9	5	NM_001271838.2	ENSP00000481697.1

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86839 AN: 151792 Hom.: 25200 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.572 AC: 86892 AN: 151910 Hom.: 25219 Cov.: 32 AF XY: 0.576 AC XY: 42760 AN XY: 74236

African (AFR) AF: 0.509 AC: 21073 AN: 41418

American (AMR) AF: 0.612 AC: 9329 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2296 AN: 3466

East Asian (EAS) AF: 0.731 AC: 3768 AN: 5158

South Asian (SAS) AF: 0.484 AC: 2331 AN: 4816

European-Finnish (FIN) AF: 0.653 AC: 6894 AN: 10550

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39035 AN: 67936

Other (OTH) AF: 0.612 AC: 1292 AN: 2112

Alfa AF: 0.550 Hom.: 10312

Bravo AF: 0.570

Asia WGS AF: 0.599 AC: 2084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.5
DANN	Benign	0.87
PhyloP100		0.19
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: rs1624094; hg19: chr3-157922110;