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.

Transcripts

RefSeq

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

Ensembl

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

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 v4.3

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;