17-1405534-A-G

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 0.738 in 152,074 control chromosomes in the GnomAD database, including 42,793 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 0.74 ( 42793 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.493
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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 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:
0.738
AC:
112086
AN:
151958
Hom.:
42726
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.930
Gnomad AMI
AF:
0.652
Gnomad AMR
AF:
0.791
Gnomad ASJ
AF:
0.667
Gnomad EAS
AF:
0.477
Gnomad SAS
AF:
0.673
Gnomad FIN
AF:
0.618
Gnomad MID
AF:
0.541
Gnomad NFE
AF:
0.658
Gnomad OTH
AF:
0.732
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.738
AC:
112218
AN:
152074
Hom.:
42793
Cov.:
31
AF XY:
0.732
AC XY:
54394
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.930
Gnomad4 AMR
AF:
0.791
Gnomad4 ASJ
AF:
0.667
Gnomad4 EAS
AF:
0.477
Gnomad4 SAS
AF:
0.672
Gnomad4 FIN
AF:
0.618
Gnomad4 NFE
AF:
0.658
Gnomad4 OTH
AF:
0.733
Alfa
AF:
0.671
Hom.:
27189
Bravo
AF:
0.757
Asia WGS
AF:
0.626
AC:
2179
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.0
DANN
Benign
0.47

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: rs1532976; hg19: chr17-1308828; API