3-158272190-T-C

Position:

• chr3-158272190-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001271838.2(RSRC1):​c.495-25849T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,910 control chromosomes in the GnomAD database, including 17,797 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 0.48 (17797 hom., cov: 32)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSRC1	NM_001271838.2	c.495-25849T>C		intron_variant		ENST00000611884.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSRC1	ENST00000611884.5	c.495-25849T>C		intron_variant		5	NM_001271838.2	P4

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72285 AN: 151792 Hom.: 17775 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.476 AC: 72354 AN: 151910 Hom.: 17797 Cov.: 32 AF XY: 0.479 AC XY: 35528 AN XY: 74228

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.494

Alfa AF: 0.433 Hom.: 24265

Bravo AF: 0.479

Asia WGS AF: 0.442 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	9.7
DANN	Benign	0.68

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: rs1213048; hg19: chr3-157989979;