rs686708

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 0.559 in 151,954 control chromosomes in the GnomAD database, including 24,876 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 0.56 ( 24876 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.940
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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.559
AC:
84832
AN:
151836
Hom.:
24837
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.730
Gnomad AMI
AF:
0.582
Gnomad AMR
AF:
0.614
Gnomad ASJ
AF:
0.659
Gnomad EAS
AF:
0.513
Gnomad SAS
AF:
0.453
Gnomad FIN
AF:
0.435
Gnomad MID
AF:
0.680
Gnomad NFE
AF:
0.466
Gnomad OTH
AF:
0.583
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.559
AC:
84931
AN:
151954
Hom.:
24876
Cov.:
32
AF XY:
0.556
AC XY:
41302
AN XY:
74250
show subpopulations
Gnomad4 AFR
AF:
0.730
Gnomad4 AMR
AF:
0.614
Gnomad4 ASJ
AF:
0.659
Gnomad4 EAS
AF:
0.513
Gnomad4 SAS
AF:
0.454
Gnomad4 FIN
AF:
0.435
Gnomad4 NFE
AF:
0.466
Gnomad4 OTH
AF:
0.582
Alfa
AF:
0.503
Hom.:
24937
Bravo
AF:
0.582
Asia WGS
AF:
0.510
AC:
1774
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
4.6
DANN
Benign
0.73

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: rs686708; hg19: chr6-117091683; API