21-10434823-T-C

Variant names:

• chr21-10434823-T-C
• rs283401
• ENST00000470054.5:n.325-19311T>C

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>C 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 0.67 (24780 hom., cov: 42)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000290523 ENST00000470054.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 1 publications found

Genes affected

ENSG00000290523 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290523	ENST00000470054.5	n.325-19311T>C		intron_variant	Intron 2 of 9	1
ENSG00000290523	ENST00000474011.5	n.380-16604T>C		intron_variant	Intron 2 of 2	2
ENSG00000290523	ENST00000807240.1	n.358-19311T>C		intron_variant	Intron 2 of 10

Frequencies

GnomAD3 genomes AF: 0.672 AC: 95804 AN: 142620 Hom.: 24769 Cov.: 42

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.711

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.662

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: 0.672 AC: 95870 AN: 142730 Hom.: 24780 Cov.: 42 AF XY: 0.673 AC XY: 46865 AN XY: 69616

African (AFR) AF: 0.541 AC: 21540 AN: 39824

American (AMR) AF: 0.713 AC: 10070 AN: 14122

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2268 AN: 3244

East Asian (EAS) AF: 0.654 AC: 3234 AN: 4942

South Asian (SAS) AF: 0.689 AC: 3067 AN: 4452

European-Finnish (FIN) AF: 0.766 AC: 7417 AN: 9688

Middle Eastern (MID) AF: 0.716 AC: 199 AN: 278

European-Non Finnish (NFE) AF: 0.730 AC: 46217 AN: 63344

Other (OTH) AF: 0.663 AC: 1314 AN: 1982

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.0
DANN	Benign	0.75
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs283401; hg19: chr21-11077634;