Variant 9-91213189-G-A 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 0.505 in 152,040 control chromosomes in the GnomAD database, including 22,006 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 0.50 ( 22006 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.156

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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.638 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:

0.505

AC:

76754

AN:

151922

Hom.:

22007

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.611

Gnomad AMR

AF:

0.642

Gnomad ASJ

AF:

0.505

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.525

Gnomad FIN

AF:

0.574

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.643

Gnomad OTH

AF:

0.533

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

GnomAD4 genome

AF:

0.505

AC:

76769

AN:

152040

Hom.:

22006

Cov.:

AF XY:

0.502

AC XY:

37309

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.231

Gnomad4 AMR

AF:

0.642

Gnomad4 ASJ

AF:

0.505

Gnomad4 EAS

AF:

0.295

Gnomad4 SAS

AF:

0.526

Gnomad4 FIN

AF:

0.574

Gnomad4 NFE

AF:

0.643

Gnomad4 OTH

AF:

0.529

Alfa

AF:

0.607

Hom.:

47397

Bravo

AF:

0.493

Asia WGS

AF:

0.392

AC:

1361

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.92

DANN

Benign

0.55

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