15-49802946-T-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 0.142 in 152,130 control chromosomes in the GnomAD database, including 1,880 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 ( 1880 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.663

Publications

0 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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 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:
0.142
AC:
21627
AN:
152012
Hom.:
1874
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0892
Gnomad AMI
AF:
0.148
Gnomad AMR
AF:
0.168
Gnomad ASJ
AF:
0.105
Gnomad EAS
AF:
0.432
Gnomad SAS
AF:
0.149
Gnomad FIN
AF:
0.162
Gnomad MID
AF:
0.149
Gnomad NFE
AF:
0.145
Gnomad OTH
AF:
0.160
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.142
AC:
21635
AN:
152130
Hom.:
1880
Cov.:
32
AF XY:
0.145
AC XY:
10778
AN XY:
74360
show subpopulations
African (AFR)
AF:
0.0890
AC:
3697
AN:
41536
American (AMR)
AF:
0.168
AC:
2577
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.105
AC:
363
AN:
3466
East Asian (EAS)
AF:
0.433
AC:
2227
AN:
5148
South Asian (SAS)
AF:
0.148
AC:
711
AN:
4812
European-Finnish (FIN)
AF:
0.162
AC:
1711
AN:
10576
Middle Eastern (MID)
AF:
0.156
AC:
46
AN:
294
European-Non Finnish (NFE)
AF:
0.145
AC:
9835
AN:
67986
Other (OTH)
AF:
0.158
AC:
334
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
911
1822
2734
3645
4556
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
244
488
732
976
1220
<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:
0.0827
Hom.:
105
Bravo
AF:
0.144
Asia WGS
AF:
0.231
AC:
799
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.81
DANN
Benign
0.69
PhyloP100
-0.66

Splicing

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

Publications

Other links and lift over

dbSNP: rs16962923; hg19: chr15-50095143; API