12-92978962-A-G

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 0.792 in 150,552 control chromosomes in the GnomAD database, including 47,952 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 0.79 ( 47952 hom., cov: 24)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.576
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.792
AC:
119103
AN:
150434
Hom.:
47882
Cov.:
24
show subpopulations
Gnomad AFR
AF:
0.945
Gnomad AMI
AF:
0.680
Gnomad AMR
AF:
0.771
Gnomad ASJ
AF:
0.660
Gnomad EAS
AF:
0.739
Gnomad SAS
AF:
0.776
Gnomad FIN
AF:
0.758
Gnomad MID
AF:
0.659
Gnomad NFE
AF:
0.724
Gnomad OTH
AF:
0.750
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.792
AC:
119228
AN:
150552
Hom.:
47952
Cov.:
24
AF XY:
0.792
AC XY:
58172
AN XY:
73426
show subpopulations
Gnomad4 AFR
AF:
0.946
Gnomad4 AMR
AF:
0.772
Gnomad4 ASJ
AF:
0.660
Gnomad4 EAS
AF:
0.739
Gnomad4 SAS
AF:
0.774
Gnomad4 FIN
AF:
0.758
Gnomad4 NFE
AF:
0.724
Gnomad4 OTH
AF:
0.753
Alfa
AF:
0.740
Hom.:
22277
Bravo
AF:
0.798
Asia WGS
AF:
0.792
AC:
2753
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
1.7
DANN
Benign
0.40

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: rs7302601; hg19: chr12-93372738; API