rs137636

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 0.404 in 151,562 control chromosomes in the GnomAD database, including 13,402 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 0.40 ( 13402 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.149
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=-0.4).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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:
0.404
AC:
61148
AN:
151446
Hom.:
13397
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.262
Gnomad AMI
AF:
0.497
Gnomad AMR
AF:
0.450
Gnomad ASJ
AF:
0.570
Gnomad EAS
AF:
0.129
Gnomad SAS
AF:
0.369
Gnomad FIN
AF:
0.422
Gnomad MID
AF:
0.478
Gnomad NFE
AF:
0.489
Gnomad OTH
AF:
0.435
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.404
AC:
61162
AN:
151562
Hom.:
13402
Cov.:
31
AF XY:
0.398
AC XY:
29444
AN XY:
74042
show subpopulations
Gnomad4 AFR
AF:
0.262
Gnomad4 AMR
AF:
0.450
Gnomad4 ASJ
AF:
0.570
Gnomad4 EAS
AF:
0.129
Gnomad4 SAS
AF:
0.368
Gnomad4 FIN
AF:
0.422
Gnomad4 NFE
AF:
0.489
Gnomad4 OTH
AF:
0.429
Alfa
AF:
0.464
Hom.:
9232
Bravo
AF:
0.399
Asia WGS
AF:
0.233
AC:
809
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
CADD
Benign
1.4
DANN
Benign
0.91

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: rs137636; hg19: chr22-39722477; API