Variant 2-151290158-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 0.686 in 152,014 control chromosomes in the GnomAD database, including 36,805 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 0.69 ( 36805 hom., cov: 33)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.582

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=-0.77).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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:

0.686

AC:

104160

AN:

151892

Hom.:

36735

Cov.:

show subpopulations

Gnomad AFR

AF:

0.863

Gnomad AMI

AF:

0.492

Gnomad AMR

AF:

0.715

Gnomad ASJ

AF:

0.524

Gnomad EAS

AF:

0.613

Gnomad SAS

AF:

0.570

Gnomad FIN

AF:

0.644

Gnomad MID

AF:

0.579

Gnomad NFE

AF:

0.604

Gnomad OTH

AF:

0.641

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.686

AC:

104285

AN:

152012

Hom.:

36805

Cov.:

AF XY:

0.686

AC XY:

50963

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.863

Gnomad4 AMR

AF:

0.715

Gnomad4 ASJ

AF:

0.524

Gnomad4 EAS

AF:

0.613

Gnomad4 SAS

AF:

0.572

Gnomad4 FIN

AF:

0.644

Gnomad4 NFE

AF:

0.604

Gnomad4 OTH

AF:

0.632

Alfa

AF:

0.605

Hom.:

38285

Bravo

AF:

0.701

Asia WGS

AF:

0.587

AC:

2044

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

2.3

DANN

Benign

0.36

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