Genetic Variant ENST00000496773.1:n.2484+666G>T (chr21-10514916-G-T) – 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 ENST00000496773.1(BAGE2):n.2484+666G>T 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 0.41 ( 299 hom., cov: 63)

Failed GnomAD Quality Control

Consequence

BAGE2
ENST00000496773.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0210

Publications

0 publications found

Variant links:

Genes affected

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:

ENSG00000273840 (HGNC:):

ENSG00000273840 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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAGE2	NR_169269.1 link	n.2243+666G>T		intron_variant	Intron 12 of 12
BAGE2	NR_169270.1 link	n.1964+666G>T		intron_variant	Intron 10 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAGE2	ENST00000496773.1 link	n.2484+666G>T		intron_variant	Intron 14 of 14	6
ENSG00000273840	ENST00000612267.1 link	n.1346+666G>T		intron_variant	Intron 10 of 31	5

Frequencies

GnomAD3 genomes

AF:

0.411

AC:

59513

AN:

144840

Hom.:

300

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.494

Gnomad AMR

AF:

0.476

Gnomad ASJ

AF:

0.466

Gnomad EAS

AF:

0.448

Gnomad SAS

AF:

0.451

Gnomad FIN

AF:

0.501

Gnomad MID

AF:

0.466

Gnomad NFE

AF:

0.493

Gnomad OTH

AF:

0.440

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: InbreedingCoeff

AF:

0.411

AC:

59543

AN:

144966

Hom.:

299

Cov.:

AF XY:

0.413

AC XY:

29286

AN XY:

70846

show subpopulations

African (AFR)

AF:

0.207

AC:

8061

AN:

38970

American (AMR)

AF:

0.476

AC:

6852

AN:

14384

Ashkenazi Jewish (ASJ)

AF:

0.466

AC:

1524

AN:

3268

East Asian (EAS)

AF:

0.448

AC:

2157

AN:

4816

South Asian (SAS)

AF:

0.451

AC:

2019

AN:

4480

European-Finnish (FIN)

AF:

0.501

AC:

5215

AN:

10400

Middle Eastern (MID)

AF:

0.461

AC:

130

AN:

282

European-Non Finnish (NFE)

AF:

0.493

AC:

32279

AN:

65512

Other (OTH)

AF:

0.441

AC:

867

AN:

1966

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.448

Heterozygous variant carriers

2309

4617

6926

9234

11543

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

728

1456

2184

2912

3640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.256

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

7.0

(source)

DANN

Benign

0.72

PhyloP100

0.021

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over