rs1915935

chr3-158186611-A-Gchr3-158186611-A-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
RSRC1	NM_001271838.2	c.321-16461A>G		intron_variant		ENST00000611884.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSRC1	ENST00000611884.5	c.321-16461A>G		intron_variant		5	NM_001271838.2	P4

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

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.684

Alfa AF: 0.647 Hom.: 4638

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1915935; hg19: chr3-157904400;