Variant chr9-22134173-C-T 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 0.451 in 151,976 control chromosomes in the GnomAD database, including 15,582 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 0.45 ( 15582 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.58

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.22134173C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.451

AC:

68532

AN:

151858

Hom.:

15561

Cov.:

show subpopulations

Gnomad AFR

AF:

0.468

Gnomad AMI

AF:

0.487

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.621

Gnomad SAS

AF:

0.442

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.429

Gnomad OTH

AF:

0.473

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

GnomAD4 genome

AF:

0.451

AC:

68593

AN:

151976

Hom.:

15582

Cov.:

AF XY:

0.453

AC XY:

33625

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.468

Gnomad4 AMR

AF:

0.431

Gnomad4 ASJ

AF:

0.459

Gnomad4 EAS

AF:

0.622

Gnomad4 SAS

AF:

0.441

Gnomad4 FIN

AF:

0.471

Gnomad4 NFE

AF:

0.429

Gnomad4 OTH

AF:

0.472

Alfa

AF:

0.446

Hom.:

27587

Bravo

AF:

0.452

Asia WGS

AF:

0.550

AC:

1914

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.082

DANN

Benign

0.53

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