Variant chr2-192576224-A-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 0.517 in 152,074 control chromosomes in the GnomAD database, including 20,397 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 0.52 ( 20397 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.226

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 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:

0.517

AC:

78520

AN:

151956

Hom.:

20372

Cov.:

show subpopulations

Gnomad AFR

AF:

0.561

Gnomad AMI

AF:

0.486

Gnomad AMR

AF:

0.457

Gnomad ASJ

AF:

0.550

Gnomad EAS

AF:

0.467

Gnomad SAS

AF:

0.501

Gnomad FIN

AF:

0.474

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.513

Gnomad OTH

AF:

0.511

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

GnomAD4 genome

AF:

0.517

AC:

78585

AN:

152074

Hom.:

20397

Cov.:

AF XY:

0.512

AC XY:

38039

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.561

Gnomad4 AMR

AF:

0.456

Gnomad4 ASJ

AF:

0.550

Gnomad4 EAS

AF:

0.467

Gnomad4 SAS

AF:

0.503

Gnomad4 FIN

AF:

0.474

Gnomad4 NFE

AF:

0.513

Gnomad4 OTH

AF:

0.516

Alfa

AF:

0.510

Hom.:

2479

Bravo

AF:

0.514

Asia WGS

AF:

0.535

AC:

1863

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.24

DANN

Benign

0.57

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