Variant 3-12004293-G-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 0.756 in 153,652 control chromosomes in the GnomAD database, including 46,413 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 0.76 ( 45563 hom., cov: 26)

Exomes 𝑓: 0.63 ( 850 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.128

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=-0.66).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.759

AC:

114193

AN:

150550

Hom.:

45550

Cov.:

show subpopulations

Gnomad AFR

AF:

0.488

Gnomad AMI

AF:

0.980

Gnomad AMR

AF:

0.829

Gnomad ASJ

AF:

0.779

Gnomad EAS

AF:

0.674

Gnomad SAS

AF:

0.875

Gnomad FIN

AF:

0.906

Gnomad MID

AF:

0.784

Gnomad NFE

AF:

0.877

Gnomad OTH

AF:

0.767

GnomAD4 exome

AF:

0.632

AC:

1890

AN:

2990

Hom.:

850

AF XY:

0.649

AC XY:

1051

AN XY:

1620

show subpopulations

Gnomad4 AFR exome

AF:

0.0804

Gnomad4 AMR exome

AF:

0.580

Gnomad4 ASJ exome

AF:

0.491

Gnomad4 EAS exome

AF:

0.255

Gnomad4 SAS exome

AF:

0.958

Gnomad4 FIN exome

AF:

0.806

Gnomad4 NFE exome

AF:

0.782

Gnomad4 OTH exome

AF:

0.605

GnomAD4 genome

AF:

0.758

AC:

114248

AN:

150662

Hom.:

45563

Cov.:

AF XY:

0.762

AC XY:

56071

AN XY:

73552

show subpopulations

Gnomad4 AFR

AF:

0.488

Gnomad4 AMR

AF:

0.830

Gnomad4 ASJ

AF:

0.779

Gnomad4 EAS

AF:

0.675

Gnomad4 SAS

AF:

0.875

Gnomad4 FIN

AF:

0.906

Gnomad4 NFE

AF:

0.877

Gnomad4 OTH

AF:

0.768

Alfa

AF:

0.788

Hom.:

4552

Bravo

AF:

0.738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

2.0

DANN

Benign

0.93

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