17-71290540-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.638 in 151,956 control chromosomes in the GnomAD database, including 33,942 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 0.64 ( 33942 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.379

Publications

4 publications found
Variant links:

Genome browser will be placed here

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.791 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:
0.639
AC:
96955
AN:
151838
Hom.:
33935
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.324
Gnomad AMI
AF:
0.866
Gnomad AMR
AF:
0.689
Gnomad ASJ
AF:
0.739
Gnomad EAS
AF:
0.738
Gnomad SAS
AF:
0.812
Gnomad FIN
AF:
0.822
Gnomad MID
AF:
0.699
Gnomad NFE
AF:
0.761
Gnomad OTH
AF:
0.653
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.638
AC:
96974
AN:
151956
Hom.:
33942
Cov.:
31
AF XY:
0.644
AC XY:
47842
AN XY:
74250
show subpopulations
African (AFR)
AF:
0.323
AC:
13389
AN:
41436
American (AMR)
AF:
0.690
AC:
10513
AN:
15238
Ashkenazi Jewish (ASJ)
AF:
0.739
AC:
2565
AN:
3472
East Asian (EAS)
AF:
0.738
AC:
3800
AN:
5150
South Asian (SAS)
AF:
0.812
AC:
3913
AN:
4818
European-Finnish (FIN)
AF:
0.822
AC:
8670
AN:
10550
Middle Eastern (MID)
AF:
0.697
AC:
205
AN:
294
European-Non Finnish (NFE)
AF:
0.761
AC:
51751
AN:
67972
Other (OTH)
AF:
0.652
AC:
1378
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1511
3022
4532
6043
7554
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
776
1552
2328
3104
3880
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.724
Hom.:
174846
Bravo
AF:
0.612
Asia WGS
AF:
0.778
AC:
2701
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
6.9
DANN
Benign
0.75
PhyloP100
-0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs11077554; hg19: chr17-69286681; API