rs1369562

Positions:

• chr3-158490771-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001271838.2(RSRC1):​c.652+29768T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,060 control chromosomes in the GnomAD database, including 20,796 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 (20796 hom., cov: 32)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSRC1	NM_001271838.2	c.652+29768T>C		intron_variant		ENST00000611884.5
RSRC1	NM_001271834.2	c.478+29768T>C		intron_variant
RSRC1	NM_016625.4	c.652+29768T>C		intron_variant
RSRC1	XM_047448275.1	c.652+29768T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSRC1	ENST00000611884.5	c.652+29768T>C		intron_variant		5	NM_001271838.2	P4

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78463 AN: 151942 Hom.: 20776 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.516 AC: 78530 AN: 152060 Hom.: 20796 Cov.: 32 AF XY: 0.517 AC XY: 38389 AN XY: 74300

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.491

Alfa AF: 0.505 Hom.: 3112

Bravo AF: 0.525

Asia WGS AF: 0.515 AC: 1790 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.29

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: rs1369562; hg19: chr3-158208560;