rs10936143

chr3-158462183-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+1180T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 151,732 control chromosomes in the GnomAD database, including 3,048 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 0.19 (3048 hom., cov: 31)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSRC1	NM_001271838.2	c.652+1180T>C		intron_variant		ENST00000611884.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSRC1	ENST00000611884.5	c.652+1180T>C		intron_variant		5	NM_001271838.2	P4

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28423 AN: 151614 Hom.: 3050 Cov.: 31

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.187 AC: 28418 AN: 151732 Hom.: 3048 Cov.: 31 AF XY: 0.187 AC XY: 13835 AN XY: 74154

Gnomad4 AFR AF: 0.0886

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0987

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.191

Alfa AF: 0.233 Hom.: 1990

Bravo AF: 0.185

Asia WGS AF: 0.183 AC: 635 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.3
Dann	Benign	0.61

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: rs10936143; hg19: chr3-158179972;