rs62408925

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 0.14 in 152,050 control chromosomes in the GnomAD database, including 1,769 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 0.14 ( 1769 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.151

Publications

2 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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 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:
0.140
AC:
21215
AN:
151932
Hom.:
1768
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0819
Gnomad AMI
AF:
0.215
Gnomad AMR
AF:
0.216
Gnomad ASJ
AF:
0.115
Gnomad EAS
AF:
0.232
Gnomad SAS
AF:
0.220
Gnomad FIN
AF:
0.211
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.134
Gnomad OTH
AF:
0.138
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.140
AC:
21230
AN:
152050
Hom.:
1769
Cov.:
32
AF XY:
0.147
AC XY:
10890
AN XY:
74298
show subpopulations
African (AFR)
AF:
0.0818
AC:
3396
AN:
41492
American (AMR)
AF:
0.217
AC:
3305
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.115
AC:
398
AN:
3472
East Asian (EAS)
AF:
0.230
AC:
1190
AN:
5166
South Asian (SAS)
AF:
0.220
AC:
1061
AN:
4816
European-Finnish (FIN)
AF:
0.211
AC:
2224
AN:
10544
Middle Eastern (MID)
AF:
0.112
AC:
33
AN:
294
European-Non Finnish (NFE)
AF:
0.134
AC:
9138
AN:
67992
Other (OTH)
AF:
0.138
AC:
290
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.515
Heterozygous variant carriers
0
921
1842
2762
3683
4604
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
248
496
744
992
1240
<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:
0.129
Hom.:
310
Bravo
AF:
0.139
Asia WGS
AF:
0.220
AC:
764
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
4.2
DANN
Benign
0.55
PhyloP100
0.15

Splicing

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

Publications

Other links and lift over

dbSNP: rs62408925; hg19: chr3-136790539; API