9-27610659-A-G

Position:

• chr9-27610659-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTAGE12P	ENST00000400348.3	n.87T>C		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.661

Gnomad4 AMR exome AF: 0.503

Gnomad4 ASJ exome AF: 0.566

Gnomad4 EAS exome AF: 0.762

Gnomad4 SAS exome AF: 0.572

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.638

Gnomad4 OTH exome AF: 0.632

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

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.641

Alfa AF: 0.629 Hom.: 43051

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2889829; hg19: chr9-27610657;