rs939114

Positions:

• chr3-158397464-C-A

Variant summary

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

The NM_001271838.2(RSRC1):​c.583+42556C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,954 control chromosomes in the GnomAD database, including 14,706 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 0.43 (14706 hom., cov: 32)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSRC1	NM_001271838.2	c.583+42556C>A		intron_variant		ENST00000611884.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSRC1	ENST00000611884.5	c.583+42556C>A		intron_variant		5	NM_001271838.2	P4

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64715 AN: 151834 Hom.: 14707 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.426 AC: 64734 AN: 151954 Hom.: 14706 Cov.: 32 AF XY: 0.426 AC XY: 31621 AN XY: 74252

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.430

Alfa AF: 0.495 Hom.: 38115

Bravo AF: 0.424

Asia WGS AF: 0.490 AC: 1700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.7
DANN	Benign	0.78

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: rs939114; hg19: chr3-158115253;