Variant chr14-55828862-G-A 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 0.466 in 152,044 control chromosomes in the GnomAD database, including 16,904 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 0.47 ( 16904 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.389

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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.643 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:

0.466

AC:

70812

AN:

151926

Hom.:

16886

Cov.:

show subpopulations

Gnomad AFR

AF:

0.400

Gnomad AMI

AF:

0.628

Gnomad AMR

AF:

0.484

Gnomad ASJ

AF:

0.537

Gnomad EAS

AF:

0.663

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.486

Gnomad OTH

AF:

0.458

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

GnomAD4 genome

AF:

0.466

AC:

70861

AN:

152044

Hom.:

16904

Cov.:

AF XY:

0.465

AC XY:

34545

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.400

Gnomad4 AMR

AF:

0.485

Gnomad4 ASJ

AF:

0.537

Gnomad4 EAS

AF:

0.662

Gnomad4 SAS

AF:

0.496

Gnomad4 FIN

AF:

0.421

Gnomad4 NFE

AF:

0.486

Gnomad4 OTH

AF:

0.458

Alfa

AF:

0.492

Hom.:

34740

Bravo

AF:

0.472

Asia WGS

AF:

0.537

AC:

1867

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.28

DANN

Benign

0.60

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