Variant rs9923476 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 0.542 in 151,996 control chromosomes in the GnomAD database, including 22,992 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 0.54 ( 22992 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.489

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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) 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:

0.542

AC:

82360

AN:

151878

Hom.:

22985

Cov.:

show subpopulations

Gnomad AFR

AF:

0.425

Gnomad AMI

AF:

0.629

Gnomad AMR

AF:

0.496

Gnomad ASJ

AF:

0.546

Gnomad EAS

AF:

0.436

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.682

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.617

Gnomad OTH

AF:

0.539

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

GnomAD4 genome

AF:

0.542

AC:

82381

AN:

151996

Hom.:

22992

Cov.:

AF XY:

0.542

AC XY:

40274

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.425

Gnomad4 AMR

AF:

0.496

Gnomad4 ASJ

AF:

0.546

Gnomad4 EAS

AF:

0.436

Gnomad4 SAS

AF:

0.422

Gnomad4 FIN

AF:

0.682

Gnomad4 NFE

AF:

0.617

Gnomad4 OTH

AF:

0.539

Alfa

AF:

0.464

Hom.:

1422

Bravo

AF:

0.522

Asia WGS

AF:

0.425

AC:

1482

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.67

DANN

Benign

0.64

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