ENST00000400348.3:n.87T>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000400348.3(CTAGE12P):​n.87T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 534,080 control chromosomes in the GnomAD database, including 105,138 homozygotes. 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 0.64 (31384 hom., cov: 34)
  • Exomes 𝑓: 0.62 (73754 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

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
There are no transcript annotations for this variant.

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97160 AN: 152036 Hom.: 31372 Cov.: 34

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.645

GnomAD4 exome AF: 0.618 AC: 235979 AN: 381926 Hom.: 73754 Cov.: 2 AF XY: 0.616 AC XY: 133291 AN XY: 216286

African (AFR) AF: 0.661 AC: 6821 AN: 10318

American (AMR) AF: 0.503 AC: 16313 AN: 32418

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 6230 AN: 11008

East Asian (EAS) AF: 0.762 AC: 11757 AN: 15438

South Asian (SAS) AF: 0.572 AC: 35894 AN: 62708

European-Finnish (FIN) AF: 0.625 AC: 19399 AN: 31060

Middle Eastern (MID) AF: 0.611 AC: 1697 AN: 2778

European-Non Finnish (NFE) AF: 0.638 AC: 126792 AN: 198674

Other (OTH) AF: 0.632 AC: 11076 AN: 17524

GnomAD4 genome AF: 0.639 AC: 97204 AN: 152154 Hom.: 31384 Cov.: 34 AF XY: 0.635 AC XY: 47262 AN XY: 74370

African (AFR) AF: 0.658 AC: 27315 AN: 41512

American (AMR) AF: 0.555 AC: 8485 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1957 AN: 3472

East Asian (EAS) AF: 0.769 AC: 3981 AN: 5174

South Asian (SAS) AF: 0.574 AC: 2767 AN: 4824

European-Finnish (FIN) AF: 0.623 AC: 6584 AN: 10568

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43893 AN: 67998

Other (OTH) AF: 0.641 AC: 1352 AN: 2110

Alfa AF: 0.636 Hom.: 95348

Bravo AF: 0.636

Asia WGS AF: 0.661 AC: 2295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.42
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;