chr10-1855784-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 0.243 in 152,190 control chromosomes in the GnomAD database, including 5,559 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 ( 5559 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.64

Publications

3 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=-0.98).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 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:
0.243
AC:
36997
AN:
152070
Hom.:
5559
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0708
Gnomad AMI
AF:
0.338
Gnomad AMR
AF:
0.288
Gnomad ASJ
AF:
0.133
Gnomad EAS
AF:
0.173
Gnomad SAS
AF:
0.201
Gnomad FIN
AF:
0.310
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.342
Gnomad OTH
AF:
0.235
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.243
AC:
37003
AN:
152190
Hom.:
5559
Cov.:
33
AF XY:
0.242
AC XY:
17976
AN XY:
74392
show subpopulations
African (AFR)
AF:
0.0706
AC:
2934
AN:
41558
American (AMR)
AF:
0.288
AC:
4406
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
0.133
AC:
463
AN:
3470
East Asian (EAS)
AF:
0.173
AC:
892
AN:
5170
South Asian (SAS)
AF:
0.201
AC:
970
AN:
4820
European-Finnish (FIN)
AF:
0.310
AC:
3279
AN:
10590
Middle Eastern (MID)
AF:
0.109
AC:
32
AN:
294
European-Non Finnish (NFE)
AF:
0.342
AC:
23226
AN:
67970
Other (OTH)
AF:
0.234
AC:
493
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1382
2764
4147
5529
6911
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
380
760
1140
1520
1900
<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:
0.232
Hom.:
1353
Bravo
AF:
0.236
Asia WGS
AF:
0.182
AC:
638
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.32
DANN
Benign
0.44
PhyloP100
-1.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs12360000; hg19: chr10-1897978; API