rs960856

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 0.441 in 152,076 control chromosomes in the GnomAD database, including 17,602 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 0.44 ( 17602 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0980

Publications

1 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=-0.56).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 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:
0.441
AC:
67024
AN:
151958
Hom.:
17553
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.745
Gnomad AMI
AF:
0.289
Gnomad AMR
AF:
0.299
Gnomad ASJ
AF:
0.301
Gnomad EAS
AF:
0.295
Gnomad SAS
AF:
0.295
Gnomad FIN
AF:
0.382
Gnomad MID
AF:
0.389
Gnomad NFE
AF:
0.329
Gnomad OTH
AF:
0.410
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.441
AC:
67132
AN:
152076
Hom.:
17602
Cov.:
33
AF XY:
0.439
AC XY:
32614
AN XY:
74348
show subpopulations
African (AFR)
AF:
0.746
AC:
30939
AN:
41478
American (AMR)
AF:
0.298
AC:
4557
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.301
AC:
1045
AN:
3470
East Asian (EAS)
AF:
0.295
AC:
1526
AN:
5168
South Asian (SAS)
AF:
0.295
AC:
1422
AN:
4820
European-Finnish (FIN)
AF:
0.382
AC:
4040
AN:
10564
Middle Eastern (MID)
AF:
0.384
AC:
113
AN:
294
European-Non Finnish (NFE)
AF:
0.329
AC:
22360
AN:
67978
Other (OTH)
AF:
0.411
AC:
867
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1669
3339
5008
6678
8347
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
584
1168
1752
2336
2920
<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:
0.184
Hom.:
362
Bravo
AF:
0.448
Asia WGS
AF:
0.330
AC:
1150
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
CADD
Benign
12
DANN
Benign
0.82
PhyloP100
-0.098

Splicing

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

Publications

Other links and lift over

dbSNP: rs960856; hg19: chr8-75894907; API