Variant chr4-154528680-C-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 0.524 in 151,836 control chromosomes in the GnomAD database, including 21,145 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 ( 21145 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0630

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 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:

0.524

AC:

79557

AN:

151718

Hom.:

21133

Cov.:

show subpopulations

Gnomad AFR

AF:

0.506

Gnomad AMI

AF:

0.486

Gnomad AMR

AF:

0.458

Gnomad ASJ

AF:

0.510

Gnomad EAS

AF:

0.691

Gnomad SAS

AF:

0.603

Gnomad FIN

AF:

0.516

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.534

Gnomad OTH

AF:

0.534

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

GnomAD4 genome

AF:

0.524

AC:

79602

AN:

151836

Hom.:

21145

Cov.:

AF XY:

0.525

AC XY:

38949

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.506

Gnomad4 AMR

AF:

0.458

Gnomad4 ASJ

AF:

0.510

Gnomad4 EAS

AF:

0.691

Gnomad4 SAS

AF:

0.603

Gnomad4 FIN

AF:

0.516

Gnomad4 NFE

AF:

0.534

Gnomad4 OTH

AF:

0.530

Alfa

AF:

0.533

Hom.:

23524

Bravo

AF:

0.518

Asia WGS

AF:

0.634

AC:

2201

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.96

DANN

Benign

0.14

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