rs9216

Variant names:

• chr5-160349040-A-G
• rs9216
• NM_031908.6:c.*128T>C

Variant summary

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

The NM_031908.6(C1QTNF2):​c.*128T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 1,112,158 control chromosomes in the GnomAD database, including 159,978 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 0.49 (19004 hom., cov: 31)
  • Exomes 𝑓: 0.54 (140974 hom.)
• Consequence: C1QTNF2 NM_031908.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 10 publications found

Genes affected

C1QTNF2 (HGNC:14325): (C1q and TNF related 2) Predicted to enable identical protein binding activity and signaling receptor binding activity. Predicted to be involved in regulation of lipid metabolic process. Predicted to act upstream of or within positive regulation of MAPK cascade; positive regulation of glucose import; and positive regulation of small molecule metabolic process. Predicted to be located in extracellular space. Predicted to be part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031908.6. 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
	C1QTNF2	NM_031908.6	MANE Select	c.*128T>C		3_prime_UTR	Exon 3 of 3	NP_114114.3
	C1QTNF2	NM_001366504.1		c.*128T>C		3_prime_UTR	Exon 4 of 4	NP_001353433.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF2	ENST00000652664.2	MANE Select	c.*128T>C		3_prime_UTR	Exon 3 of 3	ENSP00000498651.1
	C1QTNF2	ENST00000393975.4	TSL:1	c.*128T>C		3_prime_UTR	Exon 3 of 3	ENSP00000377545.3

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74572 AN: 151902 Hom.: 18998 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.508

GnomAD4 exome AF: 0.537 AC: 515142 AN: 960138 Hom.: 140974 Cov.: 12 AF XY: 0.531 AC XY: 255912 AN XY: 481670

African (AFR) AF: 0.359 AC: 8045 AN: 22428

American (AMR) AF: 0.477 AC: 12127 AN: 25406

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 8273 AN: 17250

East Asian (EAS) AF: 0.499 AC: 18244 AN: 36538

South Asian (SAS) AF: 0.360 AC: 20455 AN: 56842

European-Finnish (FIN) AF: 0.578 AC: 23134 AN: 40040

Middle Eastern (MID) AF: 0.485 AC: 1418 AN: 2922

European-Non Finnish (NFE) AF: 0.560 AC: 401055 AN: 715972

Other (OTH) AF: 0.524 AC: 22391 AN: 42740

GnomAD4 genome AF: 0.491 AC: 74599 AN: 152020 Hom.: 19004 Cov.: 31 AF XY: 0.491 AC XY: 36441 AN XY: 74282

African (AFR) AF: 0.370 AC: 15367 AN: 41480

American (AMR) AF: 0.490 AC: 7476 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1635 AN: 3466

East Asian (EAS) AF: 0.481 AC: 2480 AN: 5158

South Asian (SAS) AF: 0.363 AC: 1748 AN: 4812

European-Finnish (FIN) AF: 0.585 AC: 6179 AN: 10556

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37914 AN: 67976

Other (OTH) AF: 0.506 AC: 1067 AN: 2110

Alfa AF: 0.534 Hom.: 35629

Bravo AF: 0.482

Asia WGS AF: 0.433 AC: 1507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.2
DANN	Benign	0.80
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9216; hg19: chr5-159776047; COSMIC: COSV67432611; COSMIC: COSV67432611;