9-27610659-A-C

Variant names:

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

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>G 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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTAGE12P		n.27610659A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTAGE12P	ENST00000400348.3	n.87T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000307594	ENST00000827310.1	n.697-24273T>G		intron_variant	Intron 3 of 3
ENSG00000307594	ENST00000827311.1	n.389-24273T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 382628 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: 199028

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

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.38
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;