Variant 4-110026322-A-G 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 0.379 in 151,958 control chromosomes in the GnomAD database, including 11,498 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 0.38 ( 11498 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.650

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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.492 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:

0.379

AC:

57559

AN:

151838

Hom.:

11477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.485

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.339

Gnomad EAS

AF:

0.506

Gnomad SAS

AF:

0.438

Gnomad FIN

AF:

0.302

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.311

Gnomad OTH

AF:

0.376

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

GnomAD4 genome

AF:

0.379

AC:

57637

AN:

151958

Hom.:

11498

Cov.:

AF XY:

0.380

AC XY:

28227

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.485

Gnomad4 AMR

AF:

0.405

Gnomad4 ASJ

AF:

0.339

Gnomad4 EAS

AF:

0.508

Gnomad4 SAS

AF:

0.438

Gnomad4 FIN

AF:

0.302

Gnomad4 NFE

AF:

0.311

Gnomad4 OTH

AF:

0.378

Alfa

AF:

0.339

Hom.:

4926

Bravo

AF:

0.396

Asia WGS

AF:

0.482

AC:

1672

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.40

DANN

Benign

0.50

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