Variant chr9-21044022-T-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 0.285 in 151,684 control chromosomes in the GnomAD database, including 6,376 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 0.29 ( 6376 hom., cov: 29)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.617

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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 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:

0.285

AC:

43241

AN:

151566

Hom.:

6370

Cov.:

show subpopulations

Gnomad AFR

AF:

0.240

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.278

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.439

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.306

Gnomad OTH

AF:

0.233

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

GnomAD4 genome

AF:

0.285

AC:

43249

AN:

151684

Hom.:

6376

Cov.:

AF XY:

0.293

AC XY:

21698

AN XY:

74120

show subpopulations

Gnomad4 AFR

AF:

0.239

Gnomad4 AMR

AF:

0.254

Gnomad4 ASJ

AF:

0.232

Gnomad4 EAS

AF:

0.278

Gnomad4 SAS

AF:

0.232

Gnomad4 FIN

AF:

0.439

Gnomad4 NFE

AF:

0.306

Gnomad4 OTH

AF:

0.235

Alfa

AF:

0.229

Hom.:

765

Bravo

AF:

0.267

Asia WGS

AF:

0.238

AC:

829

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.9

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