rs17761467

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 0.118 in 152,270 control chromosomes in the GnomAD database, including 1,322 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 0.12 ( 1322 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.48
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=-0.72).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 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:
0.118
AC:
18014
AN:
152152
Hom.:
1323
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0382
Gnomad AMI
AF:
0.281
Gnomad AMR
AF:
0.108
Gnomad ASJ
AF:
0.187
Gnomad EAS
AF:
0.0693
Gnomad SAS
AF:
0.0788
Gnomad FIN
AF:
0.121
Gnomad MID
AF:
0.150
Gnomad NFE
AF:
0.169
Gnomad OTH
AF:
0.141
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.118
AC:
18015
AN:
152270
Hom.:
1322
Cov.:
32
AF XY:
0.116
AC XY:
8673
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.0381
Gnomad4 AMR
AF:
0.108
Gnomad4 ASJ
AF:
0.187
Gnomad4 EAS
AF:
0.0697
Gnomad4 SAS
AF:
0.0800
Gnomad4 FIN
AF:
0.121
Gnomad4 NFE
AF:
0.169
Gnomad4 OTH
AF:
0.140
Alfa
AF:
0.142
Hom.:
425
Bravo
AF:
0.114
Asia WGS
AF:
0.0960
AC:
336
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
14
DANN
Benign
0.81

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: rs17761467; hg19: chr17-1805677; API