chr10-5998631-G-A

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 0.403 in 151,268 control chromosomes in the GnomAD database, including 13,357 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 0.40 ( 13357 hom., cov: 29)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.252

Publications

8 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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 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:
0.403
AC:
60934
AN:
151158
Hom.:
13351
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.249
Gnomad AMI
AF:
0.714
Gnomad AMR
AF:
0.377
Gnomad ASJ
AF:
0.477
Gnomad EAS
AF:
0.385
Gnomad SAS
AF:
0.405
Gnomad FIN
AF:
0.393
Gnomad MID
AF:
0.387
Gnomad NFE
AF:
0.497
Gnomad OTH
AF:
0.406
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.403
AC:
60972
AN:
151268
Hom.:
13357
Cov.:
29
AF XY:
0.398
AC XY:
29425
AN XY:
73866
show subpopulations
African (AFR)
AF:
0.250
AC:
10301
AN:
41206
American (AMR)
AF:
0.377
AC:
5729
AN:
15196
Ashkenazi Jewish (ASJ)
AF:
0.477
AC:
1657
AN:
3472
East Asian (EAS)
AF:
0.383
AC:
1980
AN:
5168
South Asian (SAS)
AF:
0.404
AC:
1931
AN:
4782
European-Finnish (FIN)
AF:
0.393
AC:
4048
AN:
10300
Middle Eastern (MID)
AF:
0.385
AC:
111
AN:
288
European-Non Finnish (NFE)
AF:
0.497
AC:
33711
AN:
67852
Other (OTH)
AF:
0.408
AC:
856
AN:
2096
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
1734
3468
5202
6936
8670
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
578
1156
1734
2312
2890
<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:
0.347
Hom.:
1517
Bravo
AF:
0.392
Asia WGS
AF:
0.437
AC:
1519
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.2
DANN
Benign
0.54
PhyloP100
0.25

Splicing

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

Publications

Other links and lift over

dbSNP: rs7477011; hg19: chr10-6040594; API