Variant chr9-21035308-G-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 0.599 in 151,992 control chromosomes in the GnomAD database, including 27,534 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 0.60 ( 27534 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.687

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 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:

0.599

AC:

90958

AN:

151874

Hom.:

27522

Cov.:

show subpopulations

Gnomad AFR

AF:

0.550

Gnomad AMI

AF:

0.613

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.636

Gnomad EAS

AF:

0.685

Gnomad SAS

AF:

0.564

Gnomad FIN

AF:

0.637

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.642

Gnomad OTH

AF:

0.566

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

GnomAD4 genome

AF:

0.599

AC:

90995

AN:

151992

Hom.:

27534

Cov.:

AF XY:

0.598

AC XY:

44436

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.549

Gnomad4 AMR

AF:

0.490

Gnomad4 ASJ

AF:

0.636

Gnomad4 EAS

AF:

0.684

Gnomad4 SAS

AF:

0.565

Gnomad4 FIN

AF:

0.637

Gnomad4 NFE

AF:

0.642

Gnomad4 OTH

AF:

0.569

Alfa

AF:

0.621

Hom.:

3679

Bravo

AF:

0.586

Asia WGS

AF:

0.624

AC:

2172

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

DANN

Benign

0.72

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