rs10154218

Variant names:

• chr21-10462311-A-T
• rs10154218
• ENST00000470054.5:n.488-525A>T

Variant summary

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

The ENST00000470054.5(ENSG00000290523):​n.488-525A>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 0.00013 (0 hom., cov: 167)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000290523 ENST00000470054.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 0 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=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000470054.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAGE2	NR_169269.1		n.523-525A>T		intron	N/A
	BAGE2	NR_169270.1		n.523-525A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290523	ENST00000470054.5	TSL:1	n.488-525A>T		intron	N/A
	BAGE2	ENST00000496773.1	TSL:6	n.164-525A>T		intron	N/A
	ENSG00000290523	ENST00000807240.1		n.521-525A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000128 AC: 11 AN: 85862 Hom.: 0 Cov.: 167

Gnomad AFR AF: 0.000460

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: 0.000166

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000455

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: AS_VQSR AF: 0.000128 AC: 11 AN: 85900 Hom.: 0 Cov.: 167 AF XY: 0.000120 AC XY: 5 AN XY: 41670

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000459 AC: 8 AN: 17416

American (AMR) AF: 0.00 AC: 0 AN: 9728

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1994

East Asian (EAS) AF: 0.00 AC: 0 AN: 2448

South Asian (SAS) AF: 0.00 AC: 0 AN: 2334

European-Finnish (FIN) AF: 0.000166 AC: 1 AN: 6018

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 156

European-Non Finnish (NFE) AF: 0.0000455 AC: 2 AN: 43928

Other (OTH) AF: 0.00 AC: 0 AN: 1208

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.000452 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.49
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10154218; hg19: chr21-11050146;