rs10772266

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 0.462 in 150,592 control chromosomes in the GnomAD database, including 17,011 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 0.46 ( 17011 hom., cov: 30)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.22
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=-0.48).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 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:
0.462
AC:
69584
AN:
150478
Hom.:
16995
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.526
Gnomad AMI
AF:
0.403
Gnomad AMR
AF:
0.494
Gnomad ASJ
AF:
0.419
Gnomad EAS
AF:
0.904
Gnomad SAS
AF:
0.689
Gnomad FIN
AF:
0.371
Gnomad MID
AF:
0.399
Gnomad NFE
AF:
0.385
Gnomad OTH
AF:
0.414
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.462
AC:
69633
AN:
150592
Hom.:
17011
Cov.:
30
AF XY:
0.469
AC XY:
34482
AN XY:
73466
show subpopulations
Gnomad4 AFR
AF:
0.525
Gnomad4 AMR
AF:
0.495
Gnomad4 ASJ
AF:
0.419
Gnomad4 EAS
AF:
0.904
Gnomad4 SAS
AF:
0.688
Gnomad4 FIN
AF:
0.371
Gnomad4 NFE
AF:
0.385
Gnomad4 OTH
AF:
0.422
Alfa
AF:
0.406
Hom.:
1905
Bravo
AF:
0.470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
8.2
DANN
Benign
0.87

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: rs10772266; hg19: chr12-10506169; API