ENST00000400348.3:n.87T>A

Variant names:

• chr9-27610659-A-T
• rs2889829
• ENST00000400348.3:n.87T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000400348.3(CTAGE12P):​n.87T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CTAGE12P ENST00000400348.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 7 publications found

Genes affected

CTAGE12P (HGNC:37297): (CTAGE family member 12, pseudogene)

ENSG00000307594 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000400348.3. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTAGE12P	ENST00000400348.3	TSL:6	n.87T>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000307594	ENST00000827310.1		n.697-24273T>A		intron	N/A
	ENSG00000307594	ENST00000827311.1		n.389-24273T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 382626 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 216666

African (AFR) AF: 0.00 AC: 0 AN: 10336

American (AMR) AF: 0.00 AC: 0 AN: 32502

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11032

East Asian (EAS) AF: 0.00 AC: 0 AN: 15462

South Asian (SAS) AF: 0.00 AC: 0 AN: 62788

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31138

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2782

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 199026

Other (OTH) AF: 0.00 AC: 0 AN: 17560

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 95348

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.40
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2889829; hg19: chr9-27610657;