16-30904912-G-A

Variant names:

• chr16-30904912-G-A
• rs8046707

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 0.321 in 152,104 control chromosomes in the GnomAD database, including 10,438 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 (10426 hom., cov: 31)
  • Exomes 𝑓: 0.42 (12 hom.)
• Consequence: CTF2P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 13 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTF2P	ENST00000412003.1	TSL:6	n.154-114C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48815 AN: 151876 Hom.: 10424 Cov.: 31

Gnomad AFR AF: 0.0744

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.389

GnomAD4 exome AF: 0.418 AC: 46 AN: 110 Hom.: 12 AF XY: 0.407 AC XY: 35 AN XY: 86

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.750 AC: 3 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 1.00 AC: 4 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.364 AC: 32 AN: 88

Other (OTH) AF: 0.333 AC: 2 AN: 6

GnomAD4 genome AF: 0.321 AC: 48819 AN: 151994 Hom.: 10426 Cov.: 31 AF XY: 0.324 AC XY: 24066 AN XY: 74298

African (AFR) AF: 0.0742 AC: 3081 AN: 41504

American (AMR) AF: 0.392 AC: 5970 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1836 AN: 3466

East Asian (EAS) AF: 0.903 AC: 4669 AN: 5170

South Asian (SAS) AF: 0.195 AC: 939 AN: 4816

European-Finnish (FIN) AF: 0.426 AC: 4500 AN: 10564

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26455 AN: 67910

Other (OTH) AF: 0.387 AC: 819 AN: 2114

Alfa AF: 0.371 Hom.: 6369

Bravo AF: 0.320

Asia WGS AF: 0.471 AC: 1642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.61
DANN	Benign	0.63
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs8046707; hg19: chr16-30916233;