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GeneBe

rs1946518

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 0.594 in 151764 control chromosomes in the gnomAD Genomes database, including 26872 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 0.59 ( 26872 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.935

Links

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.664 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:
0.594
AC:
90083
AN:
151764
Hom.:
26872
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.640
Gnomad AMI
AF:
0.616
Gnomad AMR
AF:
0.536
Gnomad ASJ
AF:
0.488
Gnomad EAS
AF:
0.479
Gnomad SAS
AF:
0.683
Gnomad FIN
AF:
0.537
Gnomad MID
AF:
0.551
Gnomad NFE
AF:
0.595
Gnomad OTH
AF:
0.578
Alfa
AF:
0.591
Hom.:
33978
Bravo
AF:
0.593
Asia WGS
AF:
0.608
AC:
2112
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
4.5
Dann
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs1946518; hg19: chr11-112035458; API