chr10-58301486-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 0.236 in 151,852 control chromosomes in the GnomAD database, including 5,296 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 0.24 ( 5296 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23

Publications

5 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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 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:
0.236
AC:
35862
AN:
151734
Hom.:
5285
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.421
Gnomad AMI
AF:
0.140
Gnomad AMR
AF:
0.184
Gnomad ASJ
AF:
0.146
Gnomad EAS
AF:
0.311
Gnomad SAS
AF:
0.178
Gnomad FIN
AF:
0.158
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.154
Gnomad OTH
AF:
0.207
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.236
AC:
35906
AN:
151852
Hom.:
5296
Cov.:
31
AF XY:
0.236
AC XY:
17537
AN XY:
74208
show subpopulations
African (AFR)
AF:
0.421
AC:
17422
AN:
41360
American (AMR)
AF:
0.184
AC:
2810
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.146
AC:
506
AN:
3472
East Asian (EAS)
AF:
0.311
AC:
1599
AN:
5146
South Asian (SAS)
AF:
0.175
AC:
844
AN:
4816
European-Finnish (FIN)
AF:
0.158
AC:
1665
AN:
10536
Middle Eastern (MID)
AF:
0.177
AC:
52
AN:
294
European-Non Finnish (NFE)
AF:
0.154
AC:
10449
AN:
67950
Other (OTH)
AF:
0.205
AC:
432
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1264
2527
3791
5054
6318
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
370
740
1110
1480
1850
<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:
0.171
Hom.:
3002
Bravo
AF:
0.248
Asia WGS
AF:
0.239
AC:
832
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.60
DANN
Benign
0.50
PhyloP100
-1.2

Splicing

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

Publications

Other links and lift over

dbSNP: rs965867; hg19: chr10-60061246; API