Variant 3-158110533-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001271838.2(RSRC1):c.-3+310T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,596 control chromosomes in the GnomAD database, including 7,994 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 0.31 ( 7974 hom., cov: 33)

Exomes 𝑓: 0.25 ( 20 hom. )

Consequence

RSRC1
NM_001271838.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.97

Variant links:

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]

RSRC1 links:

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ACMG classification

Classification made for transcript

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 = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSRC1	NM_001271838.2 linkuse as main transcript	c.-3+310T>C		intron_variant		ENST00000611884.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSRC1	ENST00000611884.5 linkuse as main transcript	c.-3+310T>C		intron_variant		5	NM_001271838.2	P4	Q96IZ7-1

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47397

AN:

151990

Hom.:

7955

Cov.:

show subpopulations

Gnomad AFR

AF:

0.394

Gnomad AMI

AF:

0.296

Gnomad AMR

AF:

0.329

Gnomad ASJ

AF:

0.265

Gnomad EAS

AF:

0.568

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.323

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.246

Gnomad OTH

AF:

0.287

GnomAD4 exome

AF:

0.248

AC:

121

AN:

488

Hom.:

Cov.:

AF XY:

0.251

AC XY:

AN XY:

374

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.125

Gnomad4 EAS exome

AF:

0.688

Gnomad4 SAS exome

AF:

0.333

Gnomad4 FIN exome

AF:

0.265

Gnomad4 NFE exome

AF:

0.212

Gnomad4 OTH exome

AF:

0.294

GnomAD4 genome

AF:

0.312

AC:

47481

AN:

152108

Hom.:

7974

Cov.:

AF XY:

0.317

AC XY:

23543

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.394

Gnomad4 AMR

AF:

0.330

Gnomad4 ASJ

AF:

0.265

Gnomad4 EAS

AF:

0.568

Gnomad4 SAS

AF:

0.239

Gnomad4 FIN

AF:

0.323

Gnomad4 NFE

AF:

0.246

Gnomad4 OTH

AF:

0.289

Alfa

AF:

0.244

Hom.:

6936

Bravo

AF:

0.319

Asia WGS

AF:

0.384

AC:

1336

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

0.26

Dann

Benign

0.41

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over