Variant 4-27410203-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.0846 in 151,824 control chromosomes in the GnomAD database, including 594 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 0.085 ( 594 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.46

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.21).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 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:

0.0845

AC:

12826

AN:

151704

Hom.:

593

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0962

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.0827

Gnomad ASJ

AF:

0.0963

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.0731

Gnomad FIN

AF:

0.0675

Gnomad MID

AF:

0.0701

Gnomad NFE

AF:

0.0738

Gnomad OTH

AF:

0.0948

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

GnomAD4 genome

AF:

0.0846

AC:

12849

AN:

151824

Hom.:

594

Cov.:

AF XY:

0.0845

AC XY:

6268

AN XY:

74180

show subpopulations

Gnomad4 AFR

AF:

0.0962

Gnomad4 AMR

AF:

0.0829

Gnomad4 ASJ

AF:

0.0963

Gnomad4 EAS

AF:

0.146

Gnomad4 SAS

AF:

0.0735

Gnomad4 FIN

AF:

0.0675

Gnomad4 NFE

AF:

0.0738

Gnomad4 OTH

AF:

0.0953

Alfa

AF:

0.0718

Hom.:

Bravo

AF:

0.0893

Asia WGS

AF:

0.143

AC:

495

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.21

CADD

Benign

DANN

Benign

0.74

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