3-158122262-G-A

Variant names:

• chr3-158122262-G-A
• rs1204058962
• NM_001271838.2:c.158G>A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001271838.2(RSRC1):​c.158G>A​(p.Arg53Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000276 in 1,446,926 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: RSRC1 NM_001271838.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.19

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 Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3833198).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.158G>A	p.Arg53Lys	missense_variant	Exon 2 of 10	ENST00000611884.5	NP_001258767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSRC1	ENST00000611884.5	c.158G>A	p.Arg53Lys	missense_variant	Exon 2 of 10	5	NM_001271838.2	ENSP00000481697.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000276 AC: 4 AN: 1446926 Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1 AN XY: 719780

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000118

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000272

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000312 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Uncertain	0.066	T
BayesDel_noAF	Benign	-0.14
CADD	Uncertain	25
DANN	Uncertain	0.98
DEOGEN2	Benign	0.045	T;T;T;T;T;.;.;T;T
Eigen	Uncertain	0.65
Eigen_PC	Pathogenic	0.67
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.75	.;T;T;.;T;.;T;T;T
M_CAP	Benign	0.0044	T
MetaRNN	Benign	0.38	T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.45	T
MutationAssessor	Uncertain	2.3	M;.;M;M;.;M;M;.;.
PrimateAI	Uncertain	0.77	T
PROVEAN	Benign	-0.92	N;N;.;N;N;N;N;N;N
REVEL	Benign	0.17
Sift	Pathogenic	0.0	D;D;.;D;D;T;T;D;D
Sift4G	Benign	0.23	T;T;T;T;T;T;T;T;T
Polyphen		0.97	D;.;D;D;.;D;D;.;.
Vest4		0.50
MutPred		0.27		Gain of glycosylation at S50 (P = 0);Gain of glycosylation at S50 (P = 0);Gain of glycosylation at S50 (P = 0);Gain of glycosylation at S50 (P = 0);Gain of glycosylation at S50 (P = 0);Gain of glycosylation at S50 (P = 0);Gain of glycosylation at S50 (P = 0);Gain of glycosylation at S50 (P = 0);Gain of glycosylation at S50 (P = 0);
MVP		0.86
MPC		0.075
ClinPred		0.92	D
GERP RS		5.4
Varity_R		0.53
gMVP		0.35

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: rs1204058962; hg19: chr3-157840051;