rs17088439

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 0.103 in 152,186 control chromosomes in the GnomAD database, including 1,122 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 0.10 ( 1122 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.22
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 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:
0.103
AC:
15658
AN:
152068
Hom.:
1119
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.195
Gnomad AMI
AF:
0.104
Gnomad AMR
AF:
0.128
Gnomad ASJ
AF:
0.0404
Gnomad EAS
AF:
0.163
Gnomad SAS
AF:
0.110
Gnomad FIN
AF:
0.0222
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.0523
Gnomad OTH
AF:
0.102
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.103
AC:
15681
AN:
152186
Hom.:
1122
Cov.:
32
AF XY:
0.104
AC XY:
7727
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.195
Gnomad4 AMR
AF:
0.128
Gnomad4 ASJ
AF:
0.0404
Gnomad4 EAS
AF:
0.163
Gnomad4 SAS
AF:
0.109
Gnomad4 FIN
AF:
0.0222
Gnomad4 NFE
AF:
0.0523
Gnomad4 OTH
AF:
0.0992
Alfa
AF:
0.0624
Hom.:
406
Bravo
AF:
0.113
Asia WGS
AF:
0.145
AC:
503
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.17
DANN
Benign
0.75

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: rs17088439; hg19: chr18-71522091; API