Variant 9-102278981-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 0.346 in 151,906 control chromosomes in the GnomAD database, including 9,810 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 0.35 ( 9810 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.448

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=-1.03).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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:

0.345

AC:

52410

AN:

151786

Hom.:

9777

Cov.:

show subpopulations

Gnomad AFR

AF:

0.464

Gnomad AMI

AF:

0.453

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.233

Gnomad EAS

AF:

0.581

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.304

Gnomad MID

AF:

0.232

Gnomad NFE

AF:

0.267

Gnomad OTH

AF:

0.308

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

GnomAD4 genome

AF:

0.346

AC:

52487

AN:

151906

Hom.:

9810

Cov.:

AF XY:

0.349

AC XY:

25944

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.465

Gnomad4 AMR

AF:

0.324

Gnomad4 ASJ

AF:

0.233

Gnomad4 EAS

AF:

0.580

Gnomad4 SAS

AF:

0.423

Gnomad4 FIN

AF:

0.304

Gnomad4 NFE

AF:

0.267

Gnomad4 OTH

AF:

0.315

Alfa

AF:

0.277

Hom.:

8446

Bravo

AF:

0.346

Asia WGS

AF:

0.469

AC:

1634

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.59

DANN

Benign

0.24

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