Variant 4-3764028-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 0.873 in 152,182 control chromosomes in the GnomAD database, including 58,287 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 0.87 ( 58287 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.89

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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 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:

0.873

AC:

132738

AN:

152064

Hom.:

58240

Cov.:

show subpopulations

Gnomad AFR

AF:

0.900

Gnomad AMI

AF:

0.929

Gnomad AMR

AF:

0.798

Gnomad ASJ

AF:

0.882

Gnomad EAS

AF:

0.620

Gnomad SAS

AF:

0.778

Gnomad FIN

AF:

0.883

Gnomad MID

AF:

0.835

Gnomad NFE

AF:

0.896

Gnomad OTH

AF:

0.882

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

GnomAD4 genome

AF:

0.873

AC:

132840

AN:

152182

Hom.:

58287

Cov.:

AF XY:

0.868

AC XY:

64581

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.899

Gnomad4 AMR

AF:

0.798

Gnomad4 ASJ

AF:

0.882

Gnomad4 EAS

AF:

0.620

Gnomad4 SAS

AF:

0.778

Gnomad4 FIN

AF:

0.883

Gnomad4 NFE

AF:

0.896

Gnomad4 OTH

AF:

0.884

Alfa

AF:

0.887

Hom.:

83243

Bravo

AF:

0.868

Asia WGS

AF:

0.713

AC:

2482

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.056

DANN

Benign

0.26

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