16-30907166-C-G

Position:

• chr16-30907166-C-G

Variant summary

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

The ENST00000412003.1(CTF2P):​n.153+318G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,868 control chromosomes in the GnomAD database, including 10,428 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 0.32 (10428 hom., cov: 31)
• Consequence: CTF2P ENST00000412003.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 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
CTF2P	ENST00000412003.1	n.153+318G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48838 AN: 151750 Hom.: 10426 Cov.: 31

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.391

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.322 AC: 48842 AN: 151868 Hom.: 10428 Cov.: 31 AF XY: 0.324 AC XY: 24044 AN XY: 74202

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.389

Alfa AF: 0.383 Hom.: 6965

Bravo AF: 0.321

Asia WGS AF: 0.471 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11649653; hg19: chr16-30918487;