Variant 12-279491-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 0.244 in 152,124 control chromosomes in the GnomAD database, including 4,691 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 0.24 ( 4691 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.21

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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.296 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:

0.244

AC:

37071

AN:

152006

Hom.:

4682

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.182

Gnomad ASJ

AF:

0.210

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.310

Gnomad FIN

AF:

0.324

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.218

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

GnomAD4 genome

AF:

0.244

AC:

37102

AN:

152124

Hom.:

4691

Cov.:

AF XY:

0.246

AC XY:

18303

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.182

Gnomad4 ASJ

AF:

0.210

Gnomad4 EAS

AF:

0.222

Gnomad4 SAS

AF:

0.309

Gnomad4 FIN

AF:

0.324

Gnomad4 NFE

AF:

0.262

Gnomad4 OTH

AF:

0.216

Alfa

AF:

0.246

Hom.:

5050

Bravo

AF:

0.232

Asia WGS

AF:

0.257

AC:

893

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.85

DANN

Benign

0.78

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