Variant chr9-21202357-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 0.196 in 151,518 control chromosomes in the GnomAD database, including 3,212 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 0.20 ( 3212 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -6.17

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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 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:

0.196

AC:

29677

AN:

151400

Hom.:

3211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.416

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.193

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

GnomAD4 genome

AF:

0.196

AC:

29700

AN:

151518

Hom.:

3212

Cov.:

AF XY:

0.197

AC XY:

14592

AN XY:

74056

show subpopulations

Gnomad4 AFR

AF:

0.201

Gnomad4 AMR

AF:

0.247

Gnomad4 ASJ

AF:

0.199

Gnomad4 EAS

AF:

0.416

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.197

Gnomad4 NFE

AF:

0.171

Gnomad4 OTH

AF:

0.194

Alfa

AF:

0.180

Hom.:

494

Bravo

AF:

0.202

Asia WGS

AF:

0.250

AC:

867

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.075

DANN

Benign

0.40

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