Variant chr9-134545337-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 0.698 in 152,032 control chromosomes in the GnomAD database, including 37,066 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 0.70 ( 37063 hom., cov: 32)

Exomes 𝑓: 1.0 ( 3 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.321

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.134545337G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.698

AC:

106001

AN:

151908

Hom.:

37016

Cov.:

show subpopulations

Gnomad AFR

AF:

0.704

Gnomad AMI

AF:

0.719

Gnomad AMR

AF:

0.719

Gnomad ASJ

AF:

0.670

Gnomad EAS

AF:

0.750

Gnomad SAS

AF:

0.495

Gnomad FIN

AF:

0.777

Gnomad MID

AF:

0.660

Gnomad NFE

AF:

0.689

Gnomad OTH

AF:

0.679

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.698

AC:

106107

AN:

152026

Hom.:

37063

Cov.:

AF XY:

0.699

AC XY:

51958

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.704

Gnomad4 AMR

AF:

0.719

Gnomad4 ASJ

AF:

0.670

Gnomad4 EAS

AF:

0.751

Gnomad4 SAS

AF:

0.495

Gnomad4 FIN

AF:

0.777

Gnomad4 NFE

AF:

0.689

Gnomad4 OTH

AF:

0.676

Alfa

AF:

0.687

Hom.:

49002

Bravo

AF:

0.701

Asia WGS

AF:

0.638

AC:

2220

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.50

DANN

Benign

0.82

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