NM_001271838.2:c.531+4514A>G

Variant names:

• chr3-158302589-A-G
• rs864332
• NM_001271838.2:c.531+4514A>G

Variant summary

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

The NM_001271838.2(RSRC1):​c.531+4514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 128,450 control chromosomes in the GnomAD database, including 13,101 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 0.44 (13101 hom., cov: 18)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.531+4514A>G		intron_variant	Intron 5 of 9	ENST00000611884.5	NP_001258767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSRC1	ENST00000611884.5	c.531+4514A>G		intron_variant	Intron 5 of 9	5	NM_001271838.2	ENSP00000481697.1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 56235 AN: 128380 Hom.: 13092 Cov.: 18

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.457

GnomAD4 exome AF: 0.167 AC: 2 AN: 12 Hom.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.438 AC: 56265 AN: 128438 Hom.: 13101 Cov.: 18 AF XY: 0.432 AC XY: 26125 AN XY: 60504

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.456

Alfa AF: 0.440 Hom.: 2288

Bravo AF: 0.479

Asia WGS AF: 0.425 AC: 1454 AN: 3422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.84

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: rs864332; hg19: chr3-158020378;