rs57826552

chr5-34042761-AAAC-Achr5-34042761-AAAC-AAACAACchr5-34042761-AAAC-AAACAACAAC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_181435.6(C1QTNF3):c.303+59_303+61del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000788 in 1,461,886 control chromosomes in the GnomAD database, including 5 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0014 (0 hom., cov: 23)
  • Exomes 𝑓: 0.00071 (5 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 Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000711 (932/1310032) while in subpopulation EAS AF= 0.0189 (719/38032). AF 95% confidence interval is 0.0178. There are 5 homozygotes in gnomad4_exome. There are 432 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QTNF3	NM_181435.6	c.303+59_303+61del		intron_variant		ENST00000382065.8
C1QTNF3-AMACR	NR_037951.1	n.112-7006_112-7004del		intron_variant, non_coding_transcript_variant
C1QTNF3	NM_030945.4	c.84+278_84+280del		intron_variant
C1QTNF3	NR_146599.1	n.895-7006_895-7004del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1QTNF3	ENST00000382065.8	c.303+59_303+61del		intron_variant		1	NM_181435.6	P4
C1QTNF3	ENST00000231338.7	c.84+278_84+280del		intron_variant		1		A1
C1QTNF3	ENST00000508434.1	n.171+278_171+280del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00146 AC: 221 AN: 151734 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.00306

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000262

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0155

Gnomad SAS AF: 0.000625

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00240

GnomAD4 exome AF: 0.000711 AC: 932 AN: 1310032 Hom.: 5 AF XY: 0.000667 AC XY: 432 AN XY: 647266

Gnomad4 AFR exome AF: 0.00326

Gnomad4 AMR exome AF: 0.000163

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0189

Gnomad4 SAS exome AF: 0.000230

Gnomad4 FIN exome AF: 0.0000199

Gnomad4 NFE exome AF: 0.0000670

Gnomad4 OTH exome AF: 0.000573

GnomAD4 genome AF: 0.00145 AC: 220 AN: 151854 Hom.: 0 Cov.: 23 AF XY: 0.00128 AC XY: 95 AN XY: 74208

Gnomad4 AFR AF: 0.00305

Gnomad4 AMR AF: 0.000262

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0155

Gnomad4 SAS AF: 0.000626

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs57826552; hg19: chr5-34042866;