Variant 4-25065843-C-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 0.832 in 152,220 control chromosomes in the GnomAD database, including 52,815 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 0.83 ( 52815 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 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:

0.832

AC:

126617

AN:

152102

Hom.:

52763

Cov.:

show subpopulations

Gnomad AFR

AF:

0.862

Gnomad AMI

AF:

0.851

Gnomad AMR

AF:

0.840

Gnomad ASJ

AF:

0.830

Gnomad EAS

AF:

0.724

Gnomad SAS

AF:

0.846

Gnomad FIN

AF:

0.785

Gnomad MID

AF:

0.832

Gnomad NFE

AF:

0.827

Gnomad OTH

AF:

0.847

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

GnomAD4 genome

AF:

0.832

AC:

126723

AN:

152220

Hom.:

52815

Cov.:

AF XY:

0.830

AC XY:

61739

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.862

Gnomad4 AMR

AF:

0.840

Gnomad4 ASJ

AF:

0.830

Gnomad4 EAS

AF:

0.723

Gnomad4 SAS

AF:

0.847

Gnomad4 FIN

AF:

0.785

Gnomad4 NFE

AF:

0.827

Gnomad4 OTH

AF:

0.846

Alfa

AF:

0.836

Hom.:

72830

Bravo

AF:

0.837

Asia WGS

AF:

0.814

AC:

2830

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

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