chr3-158408493-T-C

Position:

• chr3-158408493-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.584-52442T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,978 control chromosomes in the GnomAD database, including 21,023 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 0.52 (21023 hom., cov: 32)
• Consequence: RSRC1 NM_001271838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSRC1	NM_001271838.2	c.584-52442T>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.584-52442T>C		intron_variant		5	NM_001271838.2	ENSP00000481697	P4

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79006 AN: 151860 Hom.: 20999 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.520 AC: 79081 AN: 151978 Hom.: 21023 Cov.: 32 AF XY: 0.517 AC XY: 38397 AN XY: 74272

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.499

Alfa AF: 0.515 Hom.: 3382

Bravo AF: 0.530

Asia WGS AF: 0.514 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.1
DANN	Benign	0.57
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs12107103; hg19: chr3-158126282;