5-34042761-AAAC-AAACAAC

Position:

• chr5-34042761-AAAC-AAACAAC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_181435.6(C1QTNF3):​c.303+61_303+62insGTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,460,992 control chromosomes in the GnomAD database, including 29,603 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.26 (6183 hom., cov: 23)
  • Exomes 𝑓: 0.18 (23420 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QTNF3	NM_181435.6	c.303+61_303+62insGTT		intron_variant		ENST00000382065.8
C1QTNF3-AMACR	NR_037951.1	n.112-7004_112-7003insGTT		intron_variant, non_coding_transcript_variant
C1QTNF3	NM_030945.4	c.84+280_84+281insGTT		intron_variant
C1QTNF3	NR_146599.1	n.895-7004_895-7003insGTT		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+62insGTT		intron_variant		1	NM_181435.6	P4
C1QTNF3	ENST00000231338.7	c.84+280_84+281insGTT		intron_variant		1		A1
C1QTNF3	ENST00000508434.1	n.171+280_171+281insGTT		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39087 AN: 151650 Hom.: 6163 Cov.: 23

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.238

GnomAD4 exome AF: 0.177 AC: 232110 AN: 1309222 Hom.: 23420 AF XY: 0.181 AC XY: 117223 AN XY: 646854

Gnomad4 AFR exome AF: 0.428

Gnomad4 AMR exome AF: 0.244

Gnomad4 ASJ exome AF: 0.183

Gnomad4 EAS exome AF: 0.425

Gnomad4 SAS exome AF: 0.336

Gnomad4 FIN exome AF: 0.173

Gnomad4 NFE exome AF: 0.146

Gnomad4 OTH exome AF: 0.205

GnomAD4 genome AF: 0.258 AC: 39144 AN: 151770 Hom.: 6183 Cov.: 23 AF XY: 0.260 AC XY: 19265 AN XY: 74160

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.240

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;