Variant 12-126496109-C-T details in Genebe, Genetics Data Aggregator

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 0.585 in 152,064 control chromosomes in the GnomAD database, including 30,186 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 ( 30186 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.151

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 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:

0.586

AC:

89002

AN:

151946

Hom.:

30176

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.703

Gnomad AMR

AF:

0.730

Gnomad ASJ

AF:

0.596

Gnomad EAS

AF:

0.901

Gnomad SAS

AF:

0.672

Gnomad FIN

AF:

0.720

Gnomad MID

AF:

0.561

Gnomad NFE

AF:

0.724

Gnomad OTH

AF:

0.607

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.585

AC:

89025

AN:

152064

Hom.:

30186

Cov.:

AF XY:

0.590

AC XY:

43859

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.730

Gnomad4 ASJ

AF:

0.596

Gnomad4 EAS

AF:

0.901

Gnomad4 SAS

AF:

0.672

Gnomad4 FIN

AF:

0.720

Gnomad4 NFE

AF:

0.724

Gnomad4 OTH

AF:

0.611

Alfa

AF:

0.684

Hom.:

33321

Bravo

AF:

0.575

Asia WGS

AF:

0.774

AC:

2691

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.7

DANN

Benign

0.48

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over