ENST00000513471.5:n.845A>G

Variant names:

• chr5-34020253-T-C
• rs840385
• ENST00000513471.5:n.845A>G

Variant summary

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

The ENST00000513471.5(C1QTNF3):​n.845A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 206,664 control chromosomes in the GnomAD database, including 22,740 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 0.46 (16796 hom., cov: 32)
  • Exomes 𝑓: 0.45 (5944 hom.)
• Consequence: C1QTNF3 ENST00000513471.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 11 publications found

Genes affected

C1QTNF3 (HGNC:14326): (C1q and TNF related 3) Enables identical protein binding activity. Involved in several processes, including cellular triglyceride homeostasis; negative regulation of NIK/NF-kappaB signaling; and regulation of cytokine production. Acts upstream of or within negative regulation of gluconeogenesis. Located in extracellular exosome and membrane. [provided by Alliance of Genome Resources, Apr 2022]

C1QTNF3-AMACR (HGNC:49198): (C1QTNF3-AMACR readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring C1q and tumor necrosis factor related protein 3 (C1QTNF3) and alpha-methylacyl-CoA racemase (AMACR) genes on chromosome 5. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus not likely to produce a protein product. [provided by RefSeq, Mar 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513471.5. 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
	C1QTNF3	NM_181435.6	MANE Select	c.*330A>G		3_prime_UTR	Exon 6 of 6	NP_852100.3
	C1QTNF3	NR_146599.1		n.1881A>G		non_coding_transcript_exon	Exon 12 of 12
	C1QTNF3	NM_030945.4		c.*330A>G		3_prime_UTR	Exon 6 of 6	NP_112207.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF3	ENST00000513471.5	TSL:1	n.845A>G		non_coding_transcript_exon	Exon 3 of 3
	C1QTNF3	ENST00000382065.8	TSL:1 MANE Select	c.*330A>G		3_prime_UTR	Exon 6 of 6	ENSP00000371497.3
	C1QTNF3	ENST00000231338.7	TSL:1	c.*330A>G		3_prime_UTR	Exon 6 of 6	ENSP00000231338.7

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69940 AN: 151876 Hom.: 16765 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.496

GnomAD4 exome AF: 0.452 AC: 24707 AN: 54670 Hom.: 5944 Cov.: 0 AF XY: 0.462 AC XY: 13201 AN XY: 28548

African (AFR) AF: 0.572 AC: 1075 AN: 1880

American (AMR) AF: 0.524 AC: 2025 AN: 3866

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 808 AN: 1920

East Asian (EAS) AF: 0.526 AC: 1853 AN: 3520

South Asian (SAS) AF: 0.720 AC: 3366 AN: 4676

European-Finnish (FIN) AF: 0.325 AC: 619 AN: 1904

Middle Eastern (MID) AF: 0.517 AC: 124 AN: 240

European-Non Finnish (NFE) AF: 0.400 AC: 13447 AN: 33622

Other (OTH) AF: 0.457 AC: 1390 AN: 3042

GnomAD4 genome AF: 0.461 AC: 70022 AN: 151994 Hom.: 16796 Cov.: 32 AF XY: 0.463 AC XY: 34386 AN XY: 74284

African (AFR) AF: 0.554 AC: 22960 AN: 41456

American (AMR) AF: 0.504 AC: 7705 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1405 AN: 3470

East Asian (EAS) AF: 0.494 AC: 2560 AN: 5178

South Asian (SAS) AF: 0.712 AC: 3430 AN: 4820

European-Finnish (FIN) AF: 0.336 AC: 3540 AN: 10522

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26829 AN: 67954

Other (OTH) AF: 0.502 AC: 1060 AN: 2110

Alfa AF: 0.416 Hom.: 17165

Bravo AF: 0.474

Asia WGS AF: 0.635 AC: 2206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.77
PhyloP100		0.035
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: rs840385; hg19: chr5-34020358;