3-158454616-T-C

Position:

• chr3-158454616-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.584-6319T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,926 control chromosomes in the GnomAD database, including 8,701 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 0.32 (8701 hom., cov: 31)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.584-6319T>C		intron_variant		ENST00000611884.5	NP_001258767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSRC1	ENST00000611884.5	c.584-6319T>C		intron_variant		5	NM_001271838.2	ENSP00000481697	P4

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49052 AN: 151810 Hom.: 8703 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.323 AC: 49063 AN: 151926 Hom.: 8701 Cov.: 31 AF XY: 0.324 AC XY: 24041 AN XY: 74268

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.337

Alfa AF: 0.389 Hom.: 21417

Bravo AF: 0.322

Asia WGS AF: 0.352 AC: 1222 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.9
DANN	Benign	0.64

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: rs10936142; hg19: chr3-158172405;