1-152914398-G-C

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 0.117 in 150,382 control chromosomes in the GnomAD database, including 1,342 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 0.12 ( 1342 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.451
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=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 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:
0.117
AC:
17513
AN:
150266
Hom.:
1337
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.216
Gnomad AMI
AF:
0.185
Gnomad AMR
AF:
0.0782
Gnomad ASJ
AF:
0.0499
Gnomad EAS
AF:
0.00138
Gnomad SAS
AF:
0.0430
Gnomad FIN
AF:
0.0590
Gnomad MID
AF:
0.141
Gnomad NFE
AF:
0.0900
Gnomad OTH
AF:
0.107
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.117
AC:
17539
AN:
150382
Hom.:
1342
Cov.:
30
AF XY:
0.112
AC XY:
8241
AN XY:
73298
show subpopulations
Gnomad4 AFR
AF:
0.216
Gnomad4 AMR
AF:
0.0780
Gnomad4 ASJ
AF:
0.0499
Gnomad4 EAS
AF:
0.00138
Gnomad4 SAS
AF:
0.0432
Gnomad4 FIN
AF:
0.0590
Gnomad4 NFE
AF:
0.0900
Gnomad4 OTH
AF:
0.106
Alfa
AF:
0.0331
Hom.:
22
Bravo
AF:
0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
0.82
DANN
Benign
0.71

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: rs34599045; hg19: chr1-152886874; API