Variant chr4-59213205-A-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 0.691 in 151,926 control chromosomes in the GnomAD database, including 36,500 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 0.69 ( 36500 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.24

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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 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:

0.690

AC:

104816

AN:

151810

Hom.:

36444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.769

Gnomad AMI

AF:

0.703

Gnomad AMR

AF:

0.616

Gnomad ASJ

AF:

0.683

Gnomad EAS

AF:

0.608

Gnomad SAS

AF:

0.702

Gnomad FIN

AF:

0.692

Gnomad MID

AF:

0.782

Gnomad NFE

AF:

0.665

Gnomad OTH

AF:

0.683

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

GnomAD4 genome

AF:

0.691

AC:

104926

AN:

151926

Hom.:

36500

Cov.:

AF XY:

0.691

AC XY:

51296

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.769

Gnomad4 AMR

AF:

0.616

Gnomad4 ASJ

AF:

0.683

Gnomad4 EAS

AF:

0.607

Gnomad4 SAS

AF:

0.701

Gnomad4 FIN

AF:

0.692

Gnomad4 NFE

AF:

0.665

Gnomad4 OTH

AF:

0.687

Alfa

AF:

0.681

Hom.:

4408

Bravo

AF:

0.684

Asia WGS

AF:

0.715

AC:

2487

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

4.2

DANN

Benign

0.68

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