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GeneBe

rs2542151

chr18-12779948-G-T

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 0.831 in 152090 control chromosomes in the gnomAD Genomes database, including 52623 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 0.83 ( 52623 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.436

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
?
GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.845 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:
0.831
AC:
126378
AN:
152090
Hom.:
52623
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.792
Gnomad AMI
AF:
0.954
Gnomad AMR
AF:
0.858
Gnomad ASJ
AF:
0.906
Gnomad EAS
AF:
0.833
Gnomad SAS
AF:
0.813
Gnomad FIN
AF:
0.861
Gnomad MID
AF:
0.864
Gnomad NFE
AF:
0.839
Gnomad OTH
AF:
0.844
Alfa
AF:
0.842
Hom.:
66884
Bravo
AF:
0.831
Asia WGS
AF:
0.816
AC:
2839
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
1.0
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: rs2542151; hg19: chr18-12779947;