Variant 7-153724234-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 0.507 in 150,042 control chromosomes in the GnomAD database, including 21,181 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 0.51 ( 21181 hom., cov: 28)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.278

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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.153724234A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287744	ENST00000665842.1 linkuse as main transcript	n.387-7783T>C		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.506

AC:

75891

AN:

149928

Hom.:

21126

Cov.:

show subpopulations

Gnomad AFR

AF:

0.720

Gnomad AMI

AF:

0.438

Gnomad AMR

AF:

0.536

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.719

Gnomad SAS

AF:

0.329

Gnomad FIN

AF:

0.492

Gnomad MID

AF:

0.376

Gnomad NFE

AF:

0.378

Gnomad OTH

AF:

0.480

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

GnomAD4 genome

AF:

0.507

AC:

76002

AN:

150042

Hom.:

21181

Cov.:

AF XY:

0.509

AC XY:

37264

AN XY:

73206

show subpopulations

Gnomad4 AFR

AF:

0.721

Gnomad4 AMR

AF:

0.537

Gnomad4 ASJ

AF:

0.398

Gnomad4 EAS

AF:

0.718

Gnomad4 SAS

AF:

0.328

Gnomad4 FIN

AF:

0.492

Gnomad4 NFE

AF:

0.378

Gnomad4 OTH

AF:

0.476

Alfa

AF:

0.452

Hom.:

2029

Bravo

AF:

0.530

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.3

DANN

Benign

0.44

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