rs2362965

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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 -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/exons	MANE	UniProt
RSRC1	NM_001271838.2	c.583+36682T>A		intron_variant		ENST00000611884.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSRC1	ENST00000611884.5	c.583+36682T>A		intron_variant		5	NM_001271838.2	P4

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

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.429

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

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: rs2362965; hg19: chr3-158109379;