rs57826552

Variant names:

• chr5-34042761-AAAC-A
• rs57826552
• NM_181435.6:c.303+59_303+61delGTT

Your query was ambiguous. Multiple possible variants found:

• chr5-34042761-AAAC-A
• chr5-34042761-AAAC-AAACAAC
• chr5-34042761-AAAC-AAACAACAAC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_181435.6(C1QTNF3):​c.303+59_303+61delGTT 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
• Publications: 3 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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population eas. GnomAdExome4 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 GnomAdExome4. There are 432 alleles in the male GnomAdExome4 subpopulation. This position passed quality control check.
• BS2: High Homozygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QTNF3	NM_181435.6	c.303+59_303+61delGTT		intron_variant	Intron 1 of 5	ENST00000382065.8	NP_852100.3
C1QTNF3	NM_030945.4	c.84+278_84+280delGTT		intron_variant	Intron 1 of 5		NP_112207.1
C1QTNF3-AMACR	NR_037951.1	n.112-7006_112-7004delGTT		intron_variant	Intron 1 of 8
C1QTNF3	NR_146599.1	n.895-7006_895-7004delGTT		intron_variant	Intron 7 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF3	ENST00000382065.8	c.303+59_303+61delGTT		intron_variant	Intron 1 of 5	1	NM_181435.6	ENSP00000371497.3
C1QTNF3	ENST00000231338.7	c.84+278_84+280delGTT		intron_variant	Intron 1 of 5	1		ENSP00000231338.7
C1QTNF3-AMACR	ENST00000382079.3	n.37-7006_37-7004delGTT		intron_variant	Intron 1 of 8	2		ENSP00000371511.3
C1QTNF3	ENST00000508434.1	n.171+278_171+280delGTT		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.00326 AC: 91 AN: 27878

American (AMR) AF: 0.000163 AC: 5 AN: 30652

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20480

East Asian (EAS) AF: 0.0189 AC: 719 AN: 38032

South Asian (SAS) AF: 0.000230 AC: 16 AN: 69462

European-Finnish (FIN) AF: 0.0000199 AC: 1 AN: 50354

Middle Eastern (MID) AF: 0.000246 AC: 1 AN: 4060

European-Non Finnish (NFE) AF: 0.0000670 AC: 68 AN: 1014994

Other (OTH) AF: 0.000573 AC: 31 AN: 54120

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

African (AFR) AF: 0.00305 AC: 126 AN: 41320

American (AMR) AF: 0.000262 AC: 4 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3458

East Asian (EAS) AF: 0.0155 AC: 80 AN: 5146

South Asian (SAS) AF: 0.000626 AC: 3 AN: 4794

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10576

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 67964

Other (OTH) AF: 0.00190 AC: 4 AN: 2108

Alfa AF: 0.00 Hom.: 44

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism

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: rs57826552; hg19: chr5-34042866;