Variant 4-154527912-T-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 0.525 in 152,018 control chromosomes in the GnomAD database, including 21,203 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 ( 21203 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.590

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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 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:

0.525

AC:

79690

AN:

151900

Hom.:

21191

Cov.:

show subpopulations

Gnomad AFR

AF:

0.507

Gnomad AMI

AF:

0.486

Gnomad AMR

AF:

0.458

Gnomad ASJ

AF:

0.509

Gnomad EAS

AF:

0.692

Gnomad SAS

AF:

0.604

Gnomad FIN

AF:

0.515

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.535

Gnomad OTH

AF:

0.536

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

GnomAD4 genome

AF:

0.525

AC:

79735

AN:

152018

Hom.:

21203

Cov.:

AF XY:

0.525

AC XY:

39010

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.507

Gnomad4 AMR

AF:

0.457

Gnomad4 ASJ

AF:

0.509

Gnomad4 EAS

AF:

0.692

Gnomad4 SAS

AF:

0.603

Gnomad4 FIN

AF:

0.515

Gnomad4 NFE

AF:

0.535

Gnomad4 OTH

AF:

0.531

Alfa

AF:

0.529

Hom.:

2045

Bravo

AF:

0.519

Asia WGS

AF:

0.635

AC:

2203

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.13

DANN

Benign

0.086

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