GeneBe

chr16-31099743-A-G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The variant allele was found at a frequency of 0.00156 in 89,942 control chromosomes in the GnomAD database, including 1 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 0.0016 ( 1 hom., cov: 23)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.832

Publications

3 publications found
Variant links:

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ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).

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:
0.00156
AC:
140
AN:
89898
Hom.:
1
Cov.:
23
show subpopulations
Gnomad AFR
AF:
0.00482
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000336
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00156
AC:
140
AN:
89942
Hom.:
1
Cov.:
23
AF XY:
0.00155
AC XY:
68
AN XY:
43866
show subpopulations
African (AFR)
AF:
0.00481
AC:
137
AN:
28462
American (AMR)
AF:
0.000336
AC:
3
AN:
8940
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2226
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4404
South Asian (SAS)
AF:
0.00
AC:
0
AN:
3460
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
4596
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
160
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
35946
Other (OTH)
AF:
0.00
AC:
0
AN:
1216
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.543
Heterozygous variant carriers
0
7
15
22
30
37
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
2
4
6
8
10
<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:
0.000222
Hom.:
0
Bravo
AF:
0.00103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.54
DANN
Benign
0.18
PhyloP100
-0.83

Splicing

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

Publications

Other links and lift over

dbSNP: rs17884388; hg19: chr16-31111064; API