Variant 11-109002392-G-A 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 0.487 in 152,118 control chromosomes in the GnomAD database, including 19,571 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 0.49 ( 19567 hom., cov: 33)

Exomes 𝑓: 0.65 ( 4 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.163

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.487

AC:

73996

AN:

151980

Hom.:

19558

Cov.:

show subpopulations

Gnomad AFR

AF:

0.273

Gnomad AMI

AF:

0.644

Gnomad AMR

AF:

0.555

Gnomad ASJ

AF:

0.645

Gnomad EAS

AF:

0.641

Gnomad SAS

AF:

0.554

Gnomad FIN

AF:

0.555

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.564

Gnomad OTH

AF:

0.508

GnomAD4 exome

AF:

0.650

AC:

AN:

Hom.:

AF XY:

0.611

AC XY:

AN XY:

show subpopulations

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.500

GnomAD4 genome

AF:

0.487

AC:

74023

AN:

152098

Hom.:

19567

Cov.:

AF XY:

0.490

AC XY:

36445

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.273

Gnomad4 AMR

AF:

0.555

Gnomad4 ASJ

AF:

0.645

Gnomad4 EAS

AF:

0.641

Gnomad4 SAS

AF:

0.555

Gnomad4 FIN

AF:

0.555

Gnomad4 NFE

AF:

0.564

Gnomad4 OTH

AF:

0.510

Alfa

AF:

0.559

Hom.:

48541

Bravo

AF:

0.474

Asia WGS

AF:

0.615

AC:

2137

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.77

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