chr12-84793732-G-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 0.564 in 151,880 control chromosomes in the GnomAD database, including 24,523 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 0.56 ( 24523 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.00
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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 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:
0.564
AC:
85641
AN:
151762
Hom.:
24497
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.551
Gnomad AMI
AF:
0.667
Gnomad AMR
AF:
0.656
Gnomad ASJ
AF:
0.610
Gnomad EAS
AF:
0.756
Gnomad SAS
AF:
0.486
Gnomad FIN
AF:
0.478
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.552
Gnomad OTH
AF:
0.582
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.564
AC:
85706
AN:
151880
Hom.:
24523
Cov.:
32
AF XY:
0.564
AC XY:
41837
AN XY:
74208
show subpopulations
Gnomad4 AFR
AF:
0.550
Gnomad4 AMR
AF:
0.656
Gnomad4 ASJ
AF:
0.610
Gnomad4 EAS
AF:
0.756
Gnomad4 SAS
AF:
0.487
Gnomad4 FIN
AF:
0.478
Gnomad4 NFE
AF:
0.552
Gnomad4 OTH
AF:
0.584
Alfa
AF:
0.553
Hom.:
12505
Bravo
AF:
0.581
Asia WGS
AF:
0.618
AC:
2146
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
3.1
DANN
Benign
0.62

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: rs4761097; hg19: chr12-85187511; API