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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_181435.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181435.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
C1QTNF3	NM_181435.6	MANE Select	c.303+56_303+61dupGTTGTT	intron	N/A	NP_852100.3	Q9BXJ4-3
C1QTNF3	NM_030945.4		c.84+275_84+280dupGTTGTT	intron	N/A	NP_112207.1	Q9BXJ4-1
C1QTNF3-AMACR	NR_037951.1		n.112-7009_112-7004dupGTTGTT	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
C1QTNF3	ENST00000382065.8	TSL:1 MANE Select	c.303+61_303+62insGTTGTT	intron	N/A	ENSP00000371497.3	Q9BXJ4-3
C1QTNF3	ENST00000231338.7	TSL:1	c.84+280_84+281insGTTGTT	intron	N/A	ENSP00000231338.7	Q9BXJ4-1
C1QTNF3-AMACR	ENST00000382079.3	TSL:2	n.37-7004_37-7003insGTTGTT	intron	N/A	ENSP00000371511.3	E9PGA6

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 v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.49

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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5-34042761-AAAC-AAACAACAAC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over