chr10-131396147-T-C

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 0.538 in 152,080 control chromosomes in the GnomAD database, including 23,680 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 0.54 ( 23680 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 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:
0.539
AC:
81845
AN:
151962
Hom.:
23676
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.347
Gnomad AMI
AF:
0.561
Gnomad AMR
AF:
0.507
Gnomad ASJ
AF:
0.561
Gnomad EAS
AF:
0.226
Gnomad SAS
AF:
0.627
Gnomad FIN
AF:
0.631
Gnomad MID
AF:
0.519
Gnomad NFE
AF:
0.664
Gnomad OTH
AF:
0.550
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.538
AC:
81879
AN:
152080
Hom.:
23680
Cov.:
33
AF XY:
0.538
AC XY:
40003
AN XY:
74348
show subpopulations
African (AFR)
AF:
0.347
AC:
14387
AN:
41446
American (AMR)
AF:
0.507
AC:
7755
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.561
AC:
1948
AN:
3470
East Asian (EAS)
AF:
0.224
AC:
1162
AN:
5176
South Asian (SAS)
AF:
0.625
AC:
3013
AN:
4818
European-Finnish (FIN)
AF:
0.631
AC:
6678
AN:
10584
Middle Eastern (MID)
AF:
0.537
AC:
158
AN:
294
European-Non Finnish (NFE)
AF:
0.664
AC:
45115
AN:
67986
Other (OTH)
AF:
0.547
AC:
1154
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1845
3690
5536
7381
9226
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
698
1396
2094
2792
3490
<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:
0.613
Hom.:
92396
Bravo
AF:
0.516
Asia WGS
AF:
0.438
AC:
1527
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.0
DANN
Benign
0.68
PhyloP100
-1.4

Splicing

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

Publications

Other links and lift over

dbSNP: rs7893895; hg19: chr10-133194410; API