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GeneBe

rs961253

chr20-6423634-C-A

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 0.332 in 151646 control chromosomes in the gnomAD Genomes database, including 8642 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 0.33 ( 8642 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.759

Links

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 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:
0.332
AC:
50406
AN:
151646
Hom.:
8642
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.350
Gnomad AMI
AF:
0.439
Gnomad AMR
AF:
0.306
Gnomad ASJ
AF:
0.327
Gnomad EAS
AF:
0.0942
Gnomad SAS
AF:
0.309
Gnomad FIN
AF:
0.290
Gnomad MID
AF:
0.331
Gnomad NFE
AF:
0.353
Gnomad OTH
AF:
0.332
Alfa
AF:
0.339
Hom.:
18851
Bravo
AF:
0.331
Asia WGS
AF:
0.246
AC:
856
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
6.8
Dann
Benign
0.45

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: rs961253; hg19: chr20-6404281;