Variant 7-150902117-A-G 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 0.477 in 151,820 control chromosomes in the GnomAD database, including 18,644 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 0.48 ( 18644 hom., cov: 30)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.549

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.150902117A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.477

AC:

72374

AN:

151702

Hom.:

18604

Cov.:

show subpopulations

Gnomad AFR

AF:

0.642

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.557

Gnomad ASJ

AF:

0.469

Gnomad EAS

AF:

0.732

Gnomad SAS

AF:

0.359

Gnomad FIN

AF:

0.417

Gnomad MID

AF:

0.395

Gnomad NFE

AF:

0.360

Gnomad OTH

AF:

0.465

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

GnomAD4 genome

AF:

0.477

AC:

72491

AN:

151820

Hom.:

18644

Cov.:

AF XY:

0.482

AC XY:

35735

AN XY:

74182

show subpopulations

Gnomad4 AFR

AF:

0.642

Gnomad4 AMR

AF:

0.558

Gnomad4 ASJ

AF:

0.469

Gnomad4 EAS

AF:

0.732

Gnomad4 SAS

AF:

0.360

Gnomad4 FIN

AF:

0.417

Gnomad4 NFE

AF:

0.360

Gnomad4 OTH

AF:

0.468

Alfa

AF:

0.391

Hom.:

16468

Bravo

AF:

0.503

Asia WGS

AF:

0.539

AC:

1872

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.2

DANN

Benign

0.75

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