Variant 12-83740041-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 0.682 in 152,064 control chromosomes in the GnomAD database, including 36,420 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 0.68 ( 36420 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.552

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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 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:

0.682

AC:

103602

AN:

151946

Hom.:

36378

Cov.:

show subpopulations

Gnomad AFR

AF:

0.804

Gnomad AMI

AF:

0.703

Gnomad AMR

AF:

0.790

Gnomad ASJ

AF:

0.751

Gnomad EAS

AF:

0.724

Gnomad SAS

AF:

0.789

Gnomad FIN

AF:

0.451

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.603

Gnomad OTH

AF:

0.710

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

GnomAD4 genome

AF:

0.682

AC:

103702

AN:

152064

Hom.:

36420

Cov.:

AF XY:

0.680

AC XY:

50536

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.804

Gnomad4 AMR

AF:

0.790

Gnomad4 ASJ

AF:

0.751

Gnomad4 EAS

AF:

0.724

Gnomad4 SAS

AF:

0.790

Gnomad4 FIN

AF:

0.451

Gnomad4 NFE

AF:

0.603

Gnomad4 OTH

AF:

0.711

Alfa

AF:

0.641

Hom.:

35755

Bravo

AF:

0.716

Asia WGS

AF:

0.713

AC:

2481

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

6.5

DANN

Benign

0.68

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