6-31243273-A-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 0.795 in 152,008 control chromosomes in the GnomAD database, including 48,024 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 0.79 ( 48024 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.22

Publications

29 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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 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:
0.795
AC:
120730
AN:
151890
Hom.:
47987
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.810
Gnomad AMI
AF:
0.837
Gnomad AMR
AF:
0.785
Gnomad ASJ
AF:
0.908
Gnomad EAS
AF:
0.764
Gnomad SAS
AF:
0.733
Gnomad FIN
AF:
0.808
Gnomad MID
AF:
0.807
Gnomad NFE
AF:
0.786
Gnomad OTH
AF:
0.801
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.795
AC:
120816
AN:
152008
Hom.:
48024
Cov.:
31
AF XY:
0.794
AC XY:
59002
AN XY:
74298
show subpopulations
African (AFR)
AF:
0.810
AC:
33527
AN:
41414
American (AMR)
AF:
0.785
AC:
11998
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.908
AC:
3152
AN:
3472
East Asian (EAS)
AF:
0.765
AC:
3958
AN:
5176
South Asian (SAS)
AF:
0.731
AC:
3516
AN:
4808
European-Finnish (FIN)
AF:
0.808
AC:
8542
AN:
10568
Middle Eastern (MID)
AF:
0.796
AC:
234
AN:
294
European-Non Finnish (NFE)
AF:
0.786
AC:
53434
AN:
67976
Other (OTH)
AF:
0.801
AC:
1693
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1301
2602
3903
5204
6505
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
872
1744
2616
3488
4360
<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:
0.797
Hom.:
92202
Bravo
AF:
0.793
Asia WGS
AF:
0.757
AC:
2634
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.39
DANN
Benign
0.32
PhyloP100
-2.2

Splicing

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

Publications

Other links and lift over

dbSNP: rs3130695; hg19: chr6-31211050; API