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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513471.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
C1QTNF3	NM_181435.6	MANE Select	c.*658G>C	3_prime_UTR	Exon 6 of 6	NP_852100.3
C1QTNF3	NR_146599.1		n.2209G>C	non_coding_transcript_exon	Exon 12 of 12
C1QTNF3	NM_030945.4		c.*658G>C	3_prime_UTR	Exon 6 of 6	NP_112207.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
C1QTNF3	ENST00000513471.5	TSL:1	n.1173G>C	non_coding_transcript_exon	Exon 3 of 3
C1QTNF3	ENST00000382065.8	TSL:1 MANE Select	c.*658G>C	3_prime_UTR	Exon 6 of 6	ENSP00000371497.3
C1QTNF3	ENST00000231338.7	TSL:1	c.*658G>C	3_prime_UTR	Exon 6 of 6	ENSP00000231338.7

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over