Variant 17-50203294-GAA-GA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.18 in 151,846 control chromosomes in the GnomAD database, including 2,574 homozygotes. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.18 ( 2574 hom., cov: 28)

Consequence

intergenic_region

Scores

Not classified

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.0550

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.50203295delA		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000249406	ENST00000509943.2 linkuse as main transcript	n.59+3361delA		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27336

AN:

151726

Hom.:

2572

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.00251

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.145

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.198

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

GnomAD4 genome

AF:

0.180

AC:

27347

AN:

151846

Hom.:

2574

Cov.:

AF XY:

0.175

AC XY:

12951

AN XY:

74196

show subpopulations

Gnomad4 AFR

AF:

0.193

Gnomad4 AMR

AF:

0.164

Gnomad4 ASJ

AF:

0.202

Gnomad4 EAS

AF:

0.00252

Gnomad4 SAS

AF:

0.128

Gnomad4 FIN

AF:

0.145

Gnomad4 NFE

AF:

0.197

Gnomad4 OTH

AF:

0.196

Alfa

AF:

0.0595

Hom.:

Bravo

AF:

0.181

Asia WGS

AF:

0.0610

AC:

213

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Bone mineral density variation quantitative trait locus

Other:1

association, no assertion criteria provided

literature only

OMIM

Aug 01, 2009

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over