rs854462

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 0.245 in 152,126 control chromosomes in the GnomAD database, including 6,446 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 ( 6446 hom., cov: 32)

Consequence

Unknown

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.590

Publications

12 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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 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:
0.244
AC:
37131
AN:
152008
Hom.:
6413
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.485
Gnomad AMI
AF:
0.0713
Gnomad AMR
AF:
0.264
Gnomad ASJ
AF:
0.135
Gnomad EAS
AF:
0.112
Gnomad SAS
AF:
0.217
Gnomad FIN
AF:
0.155
Gnomad MID
AF:
0.187
Gnomad NFE
AF:
0.129
Gnomad OTH
AF:
0.227
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.245
AC:
37230
AN:
152126
Hom.:
6446
Cov.:
32
AF XY:
0.246
AC XY:
18287
AN XY:
74376
show subpopulations
African (AFR)
AF:
0.485
AC:
20098
AN:
41444
American (AMR)
AF:
0.265
AC:
4047
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.135
AC:
468
AN:
3470
East Asian (EAS)
AF:
0.111
AC:
576
AN:
5176
South Asian (SAS)
AF:
0.216
AC:
1044
AN:
4824
European-Finnish (FIN)
AF:
0.155
AC:
1644
AN:
10600
Middle Eastern (MID)
AF:
0.184
AC:
54
AN:
294
European-Non Finnish (NFE)
AF:
0.129
AC:
8743
AN:
68008
Other (OTH)
AF:
0.233
AC:
491
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1274
2548
3823
5097
6371
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
352
704
1056
1408
1760
<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:
0.165
Hom.:
4608
Bravo
AF:
0.262

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.59
PhyloP100
-0.59

Splicing

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

Publications

Other links and lift over

dbSNP: rs854462; hg19: chr17-34386090; API