GeneBe

rs4262952

Variant names:

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 0.997 in 152,066 control chromosomes in the GnomAD database, including 75,518 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 1.0 ( 75518 hom., cov: 29)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0870

Publications

4 publications found
Variant links:

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ACMG classification

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.994 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:
0.997
AC:
151429
AN:
151948
Hom.:
75460
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.988
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.999
Gnomad ASJ
AF:
1.00
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
1.00
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
1.00
Gnomad NFE
AF:
1.00
Gnomad OTH
AF:
0.999
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.997
AC:
151545
AN:
152066
Hom.:
75518
Cov.:
29
AF XY:
0.997
AC XY:
74064
AN XY:
74308
show subpopulations
African (AFR)
AF:
0.988
AC:
40944
AN:
41454
American (AMR)
AF:
0.999
AC:
15272
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
1.00
AC:
3472
AN:
3472
East Asian (EAS)
AF:
1.00
AC:
5162
AN:
5162
South Asian (SAS)
AF:
1.00
AC:
4786
AN:
4786
European-Finnish (FIN)
AF:
1.00
AC:
10590
AN:
10590
Middle Eastern (MID)
AF:
1.00
AC:
294
AN:
294
European-Non Finnish (NFE)
AF:
1.00
AC:
68004
AN:
68004
Other (OTH)
AF:
0.999
AC:
2109
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
25
49
74
98
123
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
912
1824
2736
3648
4560
<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:
0.999
Hom.:
9419
Bravo
AF:
0.996
Asia WGS
AF:
1.00
AC:
3477
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.4
DANN
Benign
0.69
PhyloP100
-0.087

Splicing

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

Publications

Other links and lift over

dbSNP: rs4262952; hg19: chr16-26974297; API