Genetic Variant C1QTNF3:c.303+56_303+61dupGTTGTT (chr5-34042761-A-AAACAAC) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_181435.6(C1QTNF3):c.303+56_303+61dupGTTGTT 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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.493

Publications

3 publications found

Variant links:

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 links:

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]

C1QTNF3-AMACR links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
C1QTNF3	NM_181435.6 link	c.303+56_303+61dupGTTGTT	intron_variant	Intron 1 of 5	ENST00000382065.8	NP_852100.3	Q9BXJ4-3
C1QTNF3	NM_030945.4 link	c.84+275_84+280dupGTTGTT	intron_variant	Intron 1 of 5		NP_112207.1	Q9BXJ4-1
C1QTNF3-AMACR	NR_037951.1 link	n.112-7009_112-7004dupGTTGTT	intron_variant	Intron 1 of 8
C1QTNF3	NR_146599.1 link	n.895-7009_895-7004dupGTTGTT	intron_variant	Intron 7 of 11

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
C1QTNF3	ENST00000382065.8 link	c.303+61_303+62insGTTGTT	intron_variant	Intron 1 of 5	1	NM_181435.6	ENSP00000371497.3	Q9BXJ4-3
C1QTNF3	ENST00000231338.7 link	c.84+280_84+281insGTTGTT	intron_variant	Intron 1 of 5	1		ENSP00000231338.7	Q9BXJ4-1
C1QTNF3-AMACR	ENST00000382079.3 link	n.37-7004_37-7003insGTTGTT	intron_variant	Intron 1 of 8	2		ENSP00000371511.3	E9PGA6
C1QTNF3	ENST00000508434.1 link	n.171+280_171+281insGTTGTT	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.000580

AC:

AN:

151738

Hom.:

Cov.:

show subpopulations

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:

AN:

1310442

Hom.:

AF XY:

0.0000664

AC XY:

AN XY:

647482

show subpopulations

African (AFR)

AF:

0.00233

AC:

AN:

27886

American (AMR)

AF:

0.0000652

AC:

AN:

30658

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

20482

East Asian (EAS)

AF:

0.000210

AC:

AN:

38038

South Asian (SAS)

AF:

0.0000144

AC:

AN:

69470

European-Finnish (FIN)

AF:

0.00

AC:

AN:

50366

Middle Eastern (MID)

AF:

0.000492

AC:

AN:

4062

European-Non Finnish (NFE)

AF:

0.00000886

AC:

AN:

1015350

Other (OTH)

AF:

0.000166

AC:

AN:

54130

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000593

AC:

AN:

151858

Hom.:

Cov.:

AF XY:

0.000633

AC XY:

AN XY:

74210

show subpopulations

African (AFR)

AF:

0.00206

AC:

AN:

41322

American (AMR)

AF:

0.000196

AC:

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3458

East Asian (EAS)

AF:

0.000194

AC:

AN:

5148

South Asian (SAS)

AF:

0.000209

AC:

AN:

4794

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10576

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

67964

Other (OTH)

AF:

0.00

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.000661

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.49

Splicing

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

Publications

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5-34042761-AAAC-AAACAACAAC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over