Variant 9-80980146-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 0.566 in 151,956 control chromosomes in the GnomAD database, including 25,762 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 0.57 ( 25762 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.943

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 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:

0.566

AC:

85866

AN:

151838

Hom.:

25736

Cov.:

show subpopulations

Gnomad AFR

AF:

0.763

Gnomad AMI

AF:

0.312

Gnomad AMR

AF:

0.581

Gnomad ASJ

AF:

0.558

Gnomad EAS

AF:

0.712

Gnomad SAS

AF:

0.645

Gnomad FIN

AF:

0.420

Gnomad MID

AF:

0.566

Gnomad NFE

AF:

0.451

Gnomad OTH

AF:

0.577

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

GnomAD4 genome

AF:

0.566

AC:

85952

AN:

151956

Hom.:

25762

Cov.:

AF XY:

0.568

AC XY:

42152

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.763

Gnomad4 AMR

AF:

0.581

Gnomad4 ASJ

AF:

0.558

Gnomad4 EAS

AF:

0.711

Gnomad4 SAS

AF:

0.644

Gnomad4 FIN

AF:

0.420

Gnomad4 NFE

AF:

0.451

Gnomad4 OTH

AF:

0.575

Alfa

AF:

0.502

Hom.:

4706

Bravo

AF:

0.583

Asia WGS

AF:

0.686

AC:

2381

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.53

DANN

Benign

0.29

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