Variant 9-21678974-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 0.33 in 151,970 control chromosomes in the GnomAD database, including 10,836 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 0.33 ( 10836 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.30

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 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:

0.330

AC:

50043

AN:

151852

Hom.:

10811

Cov.:

show subpopulations

Gnomad AFR

AF:

0.618

Gnomad AMI

AF:

0.226

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.240

Gnomad EAS

AF:

0.403

Gnomad SAS

AF:

0.267

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.268

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.299

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

GnomAD4 genome

AF:

0.330

AC:

50119

AN:

151970

Hom.:

10836

Cov.:

AF XY:

0.329

AC XY:

24416

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.618

Gnomad4 AMR

AF:

0.268

Gnomad4 ASJ

AF:

0.240

Gnomad4 EAS

AF:

0.403

Gnomad4 SAS

AF:

0.267

Gnomad4 FIN

AF:

0.246

Gnomad4 NFE

AF:

0.187

Gnomad4 OTH

AF:

0.298

Alfa

AF:

0.257

Hom.:

944

Bravo

AF:

0.348

Asia WGS

AF:

0.330

AC:

1128

AN:

3420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

7.0

DANN

Benign

0.85

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