rs2082876

Variant summary

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

The NM_018079.5(SRBD1):​c.1874+4701G>T 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 152,038 control chromosomes in the GnomAD database, including 20,734 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 ( 20734 hom., cov: 32)

Consequence

SRBD1
NM_018079.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.193
Variant links:
Genes affected
SRBD1 (HGNC:25521): (S1 RNA binding domain 1) Predicted to enable mRNA binding activity. Predicted to be a structural constituent of ribosome. Predicted to be involved in translation. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SRBD1NM_018079.5 linkuse as main transcriptc.1874+4701G>T intron_variant ENST00000263736.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SRBD1ENST00000263736.5 linkuse as main transcriptc.1874+4701G>T intron_variant 2 NM_018079.5 P1Q8N5C6-1
SRBD1ENST00000475073.5 linkuse as main transcriptn.281+4701G>T intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.516
AC:
78439
AN:
151920
Hom.:
20722
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.555
Gnomad AMI
AF:
0.586
Gnomad AMR
AF:
0.493
Gnomad ASJ
AF:
0.479
Gnomad EAS
AF:
0.177
Gnomad SAS
AF:
0.405
Gnomad FIN
AF:
0.526
Gnomad MID
AF:
0.449
Gnomad NFE
AF:
0.531
Gnomad OTH
AF:
0.537
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.516
AC:
78494
AN:
152038
Hom.:
20734
Cov.:
32
AF XY:
0.511
AC XY:
38012
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.555
Gnomad4 AMR
AF:
0.493
Gnomad4 ASJ
AF:
0.479
Gnomad4 EAS
AF:
0.177
Gnomad4 SAS
AF:
0.406
Gnomad4 FIN
AF:
0.526
Gnomad4 NFE
AF:
0.531
Gnomad4 OTH
AF:
0.532
Alfa
AF:
0.451
Hom.:
1935
Bravo
AF:
0.513
Asia WGS
AF:
0.311
AC:
1085
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.9
DANN
Benign
0.49

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: rs2082876; hg19: chr2-45769170; API