Genetic Variant ENSG00000290523:n.325-19311T>G (chr21-10434823-T-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000470054.5(ENSG00000290523):n.325-19311T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 42)

Failed GnomAD Quality Control

Consequence

ENSG00000290523
ENST00000470054.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.03

Publications

1 publications found

Variant links:

Genes affected

ENSG00000290523 (HGNC:):

ENSG00000290523 links:

BAGE2 (HGNC:15723): (BAGE family member 2 (pseudogene)) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

BAGE2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAGE2	NR_169269.1 link	n.360-19311T>G		intron_variant	Intron 2 of 12
BAGE2	NR_169270.1 link	n.360-19311T>G		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000290523	ENST00000470054.5 link	n.325-19311T>G	intron_variant	Intron 2 of 9	1
ENSG00000290523	ENST00000474011.5 link	n.380-16604T>G	intron_variant	Intron 2 of 2	2
ENSG00000290523	ENST00000807240.1 link	n.358-19311T>G	intron_variant	Intron 2 of 10

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

143366

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

143366

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

69856

African (AFR)

AF:

0.00

AC:

AN:

40374

American (AMR)

AF:

0.00

AC:

AN:

14118

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3248

East Asian (EAS)

AF:

0.00

AC:

AN:

4962

South Asian (SAS)

AF:

0.00

AC:

AN:

4456

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9694

Middle Eastern (MID)

AF:

0.00

AC:

AN:

298

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

63396

Other (OTH)

AF:

0.00

AC:

AN:

1966

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.6

(source)

DANN

Benign

0.74

PhyloP100

-3.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over