21-10464180-C-A

Position:

• chr21-10464180-C-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_169269.1(BAGE2):​n.695-682C>A variant causes a intron, non coding transcript 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 0.052 (0 hom., cov: 205)
  • Failed GnomAD Quality Control
• Consequence: BAGE2 NR_169269.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

Genes affected

(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

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAGE2	NR_169269.1	n.695-682C>A		intron_variant, non_coding_transcript_variant
BAGE2	NR_169270.1	n.695-682C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000470054.5	n.660-682C>A		intron_variant, non_coding_transcript_variant		1
BAGE2	ENST00000496773.1	n.336-682C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 5074 AN: 98454 Hom.: 0 Cov.: 205 FAILED QC

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0180

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.0777

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.0236

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.0400

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: 0.0516 AC: 5079 AN: 98508 Hom.: 0 Cov.: 205 AF XY: 0.0523 AC XY: 2507 AN XY: 47956

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0310

Gnomad4 ASJ AF: 0.0533

Gnomad4 EAS AF: 0.0575

Gnomad4 SAS AF: 0.0770

Gnomad4 FIN AF: 0.0358

Gnomad4 NFE AF: 0.0261

Gnomad4 OTH AF: 0.0414

Alfa AF: 0.0888 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1819097; hg19: chr21-11048277;