Genetic Variant C1QTNF3:n.1173G>C (chr5-34019925-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000513471.5(C1QTNF3):n.1173G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,140 control chromosomes in the GnomAD database, including 14,880 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.43 ( 14873 hom., cov: 33)

Exomes 𝑓: 0.37 ( 7 hom. )

Consequence

C1QTNF3
ENST00000513471.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.171

Publications

7 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: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
C1QTNF3	NM_181435.6 link	c.*658G>C	3_prime_UTR_variant	Exon 6 of 6	ENST00000382065.8	NP_852100.3
C1QTNF3	NR_146599.1 link	n.2209G>C	non_coding_transcript_exon_variant	Exon 12 of 12
C1QTNF3	NM_030945.4 link	c.*658G>C	3_prime_UTR_variant	Exon 6 of 6		NP_112207.1
C1QTNF3-AMACR	NR_037951.1 link	n.764+662G>C	intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF3	ENST00000382065.8 link	c.*658G>C		3_prime_UTR_variant	Exon 6 of 6	1	NM_181435.6	ENSP00000371497.3
C1QTNF3-AMACR	ENST00000382079.3 link	n.689+662G>C		intron_variant	Intron 6 of 8	2		ENSP00000371511.3

Frequencies

GnomAD3 genomes

AF:

0.431

AC:

65426

AN:

151932

Hom.:

14843

Cov.:

show subpopulations

Gnomad AFR

AF:

0.537

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.463

Gnomad ASJ

AF:

0.354

Gnomad EAS

AF:

0.490

Gnomad SAS

AF:

0.649

Gnomad FIN

AF:

0.318

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.360

Gnomad OTH

AF:

0.450

GnomAD4 exome

AF:

0.367

AC:

AN:

Hom.:

Cov.:

AF XY:

0.313

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.341

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

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:

0.431

AC:

65509

AN:

152050

Hom.:

14873

Cov.:

AF XY:

0.433

AC XY:

32169

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.536

AC:

22243

AN:

41460

American (AMR)

AF:

0.463

AC:

7078

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.354

AC:

1229

AN:

3472

East Asian (EAS)

AF:

0.490

AC:

2537

AN:

5176

South Asian (SAS)

AF:

0.649

AC:

3133

AN:

4824

European-Finnish (FIN)

AF:

0.318

AC:

3352

AN:

10556

Middle Eastern (MID)

AF:

0.493

AC:

145

AN:

294

European-Non Finnish (NFE)

AF:

0.360

AC:

24474

AN:

67962

Other (OTH)

AF:

0.456

AC:

962

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1846

3692

5537

7383

9229

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

610

1220

1830

2440

3050

<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:

0.246

Hom.:

563

Bravo

AF:

0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.3

(source)

DANN

Benign

0.43

PhyloP100

-0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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