Variant X-126153090-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 0.0573 in 111,505 control chromosomes in the GnomAD database, including 170 homozygotes. There are 1,829 hemizygotes in GnomAD. 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 0.057 ( 170 hom., 1829 hem., cov: 22)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.681

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=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.126153090G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0573

AC:

6386

AN:

111458

Hom.:

170

Cov.:

AF XY:

0.0542

AC XY:

1828

AN XY:

33748

show subpopulations

Gnomad AFR

AF:

0.0618

Gnomad AMI

AF:

0.161

Gnomad AMR

AF:

0.0344

Gnomad ASJ

AF:

0.0625

Gnomad EAS

AF:

0.0720

Gnomad SAS

AF:

0.179

Gnomad FIN

AF:

0.0116

Gnomad MID

AF:

0.0460

Gnomad NFE

AF:

0.0559

Gnomad OTH

AF:

0.0498

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

GnomAD4 genome

AF:

0.0573

AC:

6384

AN:

111505

Hom.:

170

Cov.:

AF XY:

0.0541

AC XY:

1829

AN XY:

33805

show subpopulations

Gnomad4 AFR

AF:

0.0617

Gnomad4 AMR

AF:

0.0344

Gnomad4 ASJ

AF:

0.0625

Gnomad4 EAS

AF:

0.0716

Gnomad4 SAS

AF:

0.179

Gnomad4 FIN

AF:

0.0116

Gnomad4 NFE

AF:

0.0559

Gnomad4 OTH

AF:

0.0492

Alfa

AF:

0.0669

Hom.:

1186

Bravo

AF:

0.0589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.9

DANN

Benign

0.79

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