1-152791480-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 0.155 in 134,804 control chromosomes in the GnomAD database, including 5,756 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 0.15 ( 5756 hom., cov: 22)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.155
AC:
20828
AN:
134702
Hom.:
5744
Cov.:
22
show subpopulations
Gnomad AFR
AF:
0.386
Gnomad AMI
AF:
0.0787
Gnomad AMR
AF:
0.0909
Gnomad ASJ
AF:
0.0563
Gnomad EAS
AF:
0.0391
Gnomad SAS
AF:
0.0954
Gnomad FIN
AF:
0.0537
Gnomad MID
AF:
0.0735
Gnomad NFE
AF:
0.0599
Gnomad OTH
AF:
0.123
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.155
AC:
20867
AN:
134804
Hom.:
5756
Cov.:
22
AF XY:
0.152
AC XY:
10039
AN XY:
65844
show subpopulations
Gnomad4 AFR
AF:
0.386
Gnomad4 AMR
AF:
0.0907
Gnomad4 ASJ
AF:
0.0563
Gnomad4 EAS
AF:
0.0390
Gnomad4 SAS
AF:
0.0951
Gnomad4 FIN
AF:
0.0537
Gnomad4 NFE
AF:
0.0599
Gnomad4 OTH
AF:
0.123
Alfa
AF:
0.137
Hom.:
453
Asia WGS
AF:
0.0980
AC:
336
AN:
3416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.63
CADD
Benign
11
DANN
Benign
0.70

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: rs12086263; hg19: chr1-152763956; API