5-34042761-A-AAACAAC

Position:

• chr5-34042761-A-AAACAAC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_181435.6(C1QTNF3):​c.303+61_303+62insGTTGTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000127 in 1,462,300 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00059 (0 hom., cov: 23)
  • Exomes 𝑓: 0.000073 (0 hom.)
• Consequence: C1QTNF3 NM_181435.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

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:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QTNF3	NM_181435.6	c.303+61_303+62insGTTGTT		intron_variant		ENST00000382065.8
C1QTNF3-AMACR	NR_037951.1	n.112-7004_112-7003insGTTGTT		intron_variant, non_coding_transcript_variant
C1QTNF3	NM_030945.4	c.84+280_84+281insGTTGTT		intron_variant
C1QTNF3	NR_146599.1	n.895-7004_895-7003insGTTGTT		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1QTNF3	ENST00000382065.8	c.303+61_303+62insGTTGTT		intron_variant		1	NM_181435.6	P4
C1QTNF3	ENST00000231338.7	c.84+280_84+281insGTTGTT		intron_variant		1		A1
C1QTNF3	ENST00000508434.1	n.171+280_171+281insGTTGTT		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.000580 AC: 88 AN: 151738 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.00201

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000733 AC: 96 AN: 1310442 Hom.: 0 AF XY: 0.0000664 AC XY: 43 AN XY: 647482

Gnomad4 AFR exome AF: 0.00233

Gnomad4 AMR exome AF: 0.0000652

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000210

Gnomad4 SAS exome AF: 0.0000144

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000886

Gnomad4 OTH exome AF: 0.000166

GnomAD4 genome AF: 0.000593 AC: 90 AN: 151858 Hom.: 0 Cov.: 23 AF XY: 0.000633 AC XY: 47 AN XY: 74210

Gnomad4 AFR AF: 0.00206

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.000209

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.000661

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57826552; hg19: chr5-34042866;