rs7639867

Variant summary

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

The NM_001271838.2(RSRC1):​c.583+26479C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,038 control chromosomes in the GnomAD database, including 21,146 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 ( 21146 hom., cov: 32)

Consequence

RSRC1
NM_001271838.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.546
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RSRC1NM_001271838.2 linkuse as main transcriptc.583+26479C>A intron_variant ENST00000611884.5 NP_001258767.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RSRC1ENST00000611884.5 linkuse as main transcriptc.583+26479C>A intron_variant 5 NM_001271838.2 ENSP00000481697 P4Q96IZ7-1

Frequencies

GnomAD3 genomes
AF:
0.522
AC:
79353
AN:
151920
Hom.:
21122
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.608
Gnomad AMI
AF:
0.287
Gnomad AMR
AF:
0.519
Gnomad ASJ
AF:
0.474
Gnomad EAS
AF:
0.371
Gnomad SAS
AF:
0.599
Gnomad FIN
AF:
0.387
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:
0.522
AC:
79425
AN:
152038
Hom.:
21146
Cov.:
32
AF XY:
0.519
AC XY:
38601
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.608
Gnomad4 AMR
AF:
0.519
Gnomad4 ASJ
AF:
0.474
Gnomad4 EAS
AF:
0.371
Gnomad4 SAS
AF:
0.598
Gnomad4 FIN
AF:
0.387
Gnomad4 NFE
AF:
0.504
Gnomad4 OTH
AF:
0.499
Alfa
AF:
0.500
Hom.:
7961
Bravo
AF:
0.533
Asia WGS
AF:
0.523
AC:
1819
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
1.2
DANN
Benign
0.52

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.

Other links and lift over

dbSNP: rs7639867; hg19: chr3-158099176; API