rs26438

Variant summary

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

The variant allele was found at a frequency of 0.483 in 151,806 control chromosomes in the GnomAD database, including 18,453 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 ( 18453 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.443
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.483
AC:
73280
AN:
151688
Hom.:
18416
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.545
Gnomad AMI
AF:
0.458
Gnomad AMR
AF:
0.554
Gnomad ASJ
AF:
0.321
Gnomad EAS
AF:
0.707
Gnomad SAS
AF:
0.632
Gnomad FIN
AF:
0.522
Gnomad MID
AF:
0.468
Gnomad NFE
AF:
0.406
Gnomad OTH
AF:
0.449
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.483
AC:
73366
AN:
151806
Hom.:
18453
Cov.:
32
AF XY:
0.493
AC XY:
36555
AN XY:
74170
show subpopulations
Gnomad4 AFR
AF:
0.545
Gnomad4 AMR
AF:
0.554
Gnomad4 ASJ
AF:
0.321
Gnomad4 EAS
AF:
0.707
Gnomad4 SAS
AF:
0.630
Gnomad4 FIN
AF:
0.522
Gnomad4 NFE
AF:
0.406
Gnomad4 OTH
AF:
0.455
Alfa
AF:
0.420
Hom.:
18466
Bravo
AF:
0.485
Asia WGS
AF:
0.652
AC:
2265
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
7.3
DANN
Benign
0.50

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: rs26438; hg19: chr5-165288921; API