chr3-158312454-T-C

Position:

• chr3-158312454-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.531+14379T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,004 control chromosomes in the GnomAD database, including 18,261 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 (18261 hom., cov: 32)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.531+14379T>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.531+14379T>C		intron_variant		5	NM_001271838.2	ENSP00000481697	P4

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73133 AN: 151884 Hom.: 18239 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.482 AC: 73202 AN: 152004 Hom.: 18261 Cov.: 32 AF XY: 0.483 AC XY: 35916 AN XY: 74296

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.496

Alfa AF: 0.452 Hom.: 2693

Bravo AF: 0.485

Asia WGS AF: 0.444 AC: 1544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.54

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: rs1193509; hg19: chr3-158030243;