16-30907166-C-G

Variant names:

• chr16-30907166-C-G
• rs11649653

Variant summary

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

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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 82 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412003.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTF2P	ENST00000412003.1	TSL:6	n.153+318G>C		intron	N/A

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

African (AFR) AF: 0.0762 AC: 3159 AN: 41434

American (AMR) AF: 0.392 AC: 5976 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1820 AN: 3466

East Asian (EAS) AF: 0.904 AC: 4655 AN: 5150

South Asian (SAS) AF: 0.196 AC: 944 AN: 4810

European-Finnish (FIN) AF: 0.423 AC: 4457 AN: 10548

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26459 AN: 67904

Other (OTH) AF: 0.389 AC: 818 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.5
DANN	Benign	0.72
PhyloP100		0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11649653;

hg19: chr16-30918487;