6-31575287-A-G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The variant allele was found at a frequency of 0.0000146 in 478,892 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000026 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000092 ( 0 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0230
Publications
5 publications found
Genome browser will be placed here
ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Variant Effect in Transcripts
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|
Frequencies
GnomAD3 genomes 0.0000263 AC: 4AN: 152178Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
4
AN:
152178
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0000139 AC: 2AN: 143782 AF XY: 0.0000256 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
143782
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000918 AC: 3AN: 326714Hom.: 0 Cov.: 0 AF XY: 0.0000162 AC XY: 3AN XY: 184980 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
326714
Hom.:
Cov.:
0
AF XY:
AC XY:
3
AN XY:
184980
show subpopulations
African (AFR)
AF:
AC:
0
AN:
9538
American (AMR)
AF:
AC:
0
AN:
28340
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
11552
East Asian (EAS)
AF:
AC:
0
AN:
10870
South Asian (SAS)
AF:
AC:
0
AN:
60050
European-Finnish (FIN)
AF:
AC:
0
AN:
14200
Middle Eastern (MID)
AF:
AC:
0
AN:
2852
European-Non Finnish (NFE)
AF:
AC:
2
AN:
173614
Other (OTH)
AF:
AC:
0
AN:
15698
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.408
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000263 AC: 4AN: 152178Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74348 show subpopulations
GnomAD4 genome
AF:
AC:
4
AN:
152178
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
74348
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41444
American (AMR)
AF:
AC:
0
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5198
South Asian (SAS)
AF:
AC:
0
AN:
4828
European-Finnish (FIN)
AF:
AC:
0
AN:
10620
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
4
AN:
68012
Other (OTH)
AF:
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
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:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.