Variant 9-21228286-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 0.173 in 1,423,496 control chromosomes in the GnomAD database, including 23,438 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 0.19 ( 3125 hom., cov: 32)

Exomes 𝑓: 0.17 ( 20313 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.96

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 = 0.402 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:

0.194

AC:

29511

AN:

151886

Hom.:

3123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.246

Gnomad ASJ

AF:

0.200

Gnomad EAS

AF:

0.417

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.190

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.193

GnomAD4 exome

AF:

0.170

AC:

216102

AN:

1271494

Hom.:

20313

AF XY:

0.168

AC XY:

104282

AN XY:

619586

show subpopulations

Gnomad4 AFR exome

AF:

0.198

Gnomad4 AMR exome

AF:

0.260

Gnomad4 ASJ exome

AF:

0.190

Gnomad4 EAS exome

AF:

0.432

Gnomad4 SAS exome

AF:

0.110

Gnomad4 FIN exome

AF:

0.180

Gnomad4 NFE exome

AF:

0.160

Gnomad4 OTH exome

AF:

0.176

GnomAD4 genome

AF:

0.194

AC:

29537

AN:

152002

Hom.:

3125

Cov.:

AF XY:

0.195

AC XY:

14498

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.202

Gnomad4 AMR

AF:

0.246

Gnomad4 ASJ

AF:

0.200

Gnomad4 EAS

AF:

0.417

Gnomad4 SAS

AF:

0.113

Gnomad4 FIN

AF:

0.190

Gnomad4 NFE

AF:

0.168

Gnomad4 OTH

AF:

0.193

Alfa

AF:

0.186

Hom.:

330

Bravo

AF:

0.202

Asia WGS

AF:

0.249

AC:

866

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.048

DANN

Benign

0.73

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