15-23893158-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.816 in 151,946 control chromosomes in the GnomAD database, including 51,225 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 0.82 ( 51225 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.217
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.816
AC:
123908
AN:
151828
Hom.:
51204
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.668
Gnomad AMI
AF:
0.927
Gnomad AMR
AF:
0.881
Gnomad ASJ
AF:
0.856
Gnomad EAS
AF:
0.989
Gnomad SAS
AF:
0.856
Gnomad FIN
AF:
0.811
Gnomad MID
AF:
0.861
Gnomad NFE
AF:
0.872
Gnomad OTH
AF:
0.844
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.816
AC:
123973
AN:
151946
Hom.:
51225
Cov.:
31
AF XY:
0.817
AC XY:
60667
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.668
Gnomad4 AMR
AF:
0.881
Gnomad4 ASJ
AF:
0.856
Gnomad4 EAS
AF:
0.989
Gnomad4 SAS
AF:
0.856
Gnomad4 FIN
AF:
0.811
Gnomad4 NFE
AF:
0.872
Gnomad4 OTH
AF:
0.845
Alfa
AF:
0.861
Hom.:
77603
Bravo
AF:
0.817
Asia WGS
AF:
0.904
AC:
3146
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
4.8
DANN
Benign
0.44

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10162946; hg19: chr15-24138305; API