21-10434823-T-C

Position:

• chr21-10434823-T-C

Variant summary

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

The NR_169269.1(BAGE2):​n.360-19311T>C 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 0.67 (24780 hom., cov: 42)
  • Failed GnomAD Quality Control
• Consequence: BAGE2 NR_169269.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAGE2	NR_169269.1	n.360-19311T>C		intron_variant, non_coding_transcript_variant
BAGE2	NR_169270.1	n.360-19311T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000470054.5	n.325-19311T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000474011.5	n.380-16604T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 95804 AN: 142620 Hom.: 24769 Cov.: 42 FAILED QC

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

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.663

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs283401; hg19: chr21-11077634;