chr5-34020253-T-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000513471.5(C1QTNF3):​n.845A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).

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>T		3_prime_UTR	Exon 6 of 6	NP_852100.3
	C1QTNF3	NR_146599.1		n.1881A>T		non_coding_transcript_exon	Exon 12 of 12
	C1QTNF3	NM_030945.4		c.*330A>T		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>T		non_coding_transcript_exon	Exon 3 of 3
	C1QTNF3	ENST00000382065.8	TSL:1 MANE Select	c.*330A>T		3_prime_UTR	Exon 6 of 6	ENSP00000371497.3
	C1QTNF3	ENST00000231338.7	TSL:1	c.*330A>T		3_prime_UTR	Exon 6 of 6	ENSP00000231338.7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 54862 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 28652

African (AFR) AF: 0.00 AC: 0 AN: 1890

American (AMR) AF: 0.00 AC: 0 AN: 3876

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1924

East Asian (EAS) AF: 0.00 AC: 0 AN: 3532

South Asian (SAS) AF: 0.00 AC: 0 AN: 4686

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1908

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 240

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 33754

Other (OTH) AF: 0.00 AC: 0 AN: 3052

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 17165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.6
DANN	Benign	0.78
PhyloP100		0.035

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;