rs1369562

Variant summary

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

The NM_001271838.2(RSRC1):​c.652+29768T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,060 control chromosomes in the GnomAD database, including 20,796 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 ( 20796 hom., cov: 32)

Consequence

RSRC1
NM_001271838.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0440
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]

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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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RSRC1NM_001271838.2 linkuse as main transcriptc.652+29768T>C intron_variant ENST00000611884.5
RSRC1NM_001271834.2 linkuse as main transcriptc.478+29768T>C intron_variant
RSRC1NM_016625.4 linkuse as main transcriptc.652+29768T>C intron_variant
RSRC1XM_047448275.1 linkuse as main transcriptc.652+29768T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RSRC1ENST00000611884.5 linkuse as main transcriptc.652+29768T>C intron_variant 5 NM_001271838.2 P4Q96IZ7-1

Frequencies

GnomAD3 genomes
AF:
0.516
AC:
78463
AN:
151942
Hom.:
20776
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.628
Gnomad AMI
AF:
0.378
Gnomad AMR
AF:
0.511
Gnomad ASJ
AF:
0.427
Gnomad EAS
AF:
0.326
Gnomad SAS
AF:
0.606
Gnomad FIN
AF:
0.425
Gnomad MID
AF:
0.566
Gnomad NFE
AF:
0.479
Gnomad OTH
AF:
0.488
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.516
AC:
78530
AN:
152060
Hom.:
20796
Cov.:
32
AF XY:
0.517
AC XY:
38389
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.628
Gnomad4 AMR
AF:
0.510
Gnomad4 ASJ
AF:
0.427
Gnomad4 EAS
AF:
0.326
Gnomad4 SAS
AF:
0.605
Gnomad4 FIN
AF:
0.425
Gnomad4 NFE
AF:
0.479
Gnomad4 OTH
AF:
0.491
Alfa
AF:
0.505
Hom.:
3112
Bravo
AF:
0.525
Asia WGS
AF:
0.515
AC:
1790
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
4.6
DANN
Benign
0.29

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: rs1369562; hg19: chr3-158208560; API