chr16-30904808-G-A

Position:

• chr16-30904808-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412003.1(CTF2P):​n.154-10C>T variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,490 control chromosomes in the GnomAD database, including 4,405 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 0.22 (4399 hom., cov: 33)
  • Exomes 𝑓: 0.22 (6 hom.)
• Consequence: CTF2P ENST00000412003.1 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

Genes affected

CTF2P (HGNC:33173): (cardiotrophin 2, pseudogene) The cytokine neuropoietin belongs to the IL-6 superfamily. This gene has been inactivated by mutation and is nonfunctional in humans. [provided by RefSeq, Mar 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTF2P	ENST00000412003.1	n.154-10C>T		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32848 AN: 152082 Hom.: 4399 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.217

GnomAD4 exome AF: 0.221 AC: 64 AN: 290 Hom.: 6 Cov.: 0 AF XY: 0.215 AC XY: 43 AN XY: 200

Gnomad4 AFR exome AF: 0.125

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.196

Gnomad4 NFE exome AF: 0.233

Gnomad4 OTH exome AF: 0.136

GnomAD4 genome AF: 0.216 AC: 32860 AN: 152200 Hom.: 4399 Cov.: 33 AF XY: 0.225 AC XY: 16738 AN XY: 74412

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0870

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.222

Alfa AF: 0.218 Hom.: 3617

Bravo AF: 0.203

Asia WGS AF: 0.383 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	5.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458201; hg19: chr16-30916129;