rs634990

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.481 in 151,998 control chromosomes in the GnomAD database, including 17,728 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 0.48 ( 17728 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0740
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.481
AC:
73024
AN:
151880
Hom.:
17713
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.517
Gnomad AMI
AF:
0.737
Gnomad AMR
AF:
0.456
Gnomad ASJ
AF:
0.400
Gnomad EAS
AF:
0.451
Gnomad SAS
AF:
0.615
Gnomad FIN
AF:
0.343
Gnomad MID
AF:
0.427
Gnomad NFE
AF:
0.480
Gnomad OTH
AF:
0.480
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.481
AC:
73075
AN:
151998
Hom.:
17728
Cov.:
32
AF XY:
0.475
AC XY:
35278
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.517
Gnomad4 AMR
AF:
0.456
Gnomad4 ASJ
AF:
0.400
Gnomad4 EAS
AF:
0.451
Gnomad4 SAS
AF:
0.615
Gnomad4 FIN
AF:
0.343
Gnomad4 NFE
AF:
0.480
Gnomad4 OTH
AF:
0.480
Alfa
AF:
0.474
Hom.:
31010
Bravo
AF:
0.486
Asia WGS
AF:
0.532
AC:
1852
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.34
CADD
Benign
15
DANN
Benign
0.70

Splicing

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: rs634990; hg19: chr15-35006073; API