Genetic Variant ENST00000513471.5:n.926G>A (chr5-34020172-C-T) – 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.926G>A 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 0.393 in 165,080 control chromosomes in the GnomAD database, including 13,265 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 0.39 ( 11966 hom., cov: 32)

Exomes 𝑓: 0.43 ( 1299 hom. )

Consequence

C1QTNF3
ENST00000513471.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.232

Publications

13 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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
C1QTNF3	NM_181435.6 link	c.*411G>A	3_prime_UTR_variant	Exon 6 of 6	ENST00000382065.8	NP_852100.3
C1QTNF3	NR_146599.1 link	n.1962G>A	non_coding_transcript_exon_variant	Exon 12 of 12
C1QTNF3	NM_030945.4 link	c.*411G>A	3_prime_UTR_variant	Exon 6 of 6		NP_112207.1
C1QTNF3-AMACR	NR_037951.1 link	n.764+415G>A	intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF3	ENST00000382065.8 link	c.*411G>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_181435.6	ENSP00000371497.3
C1QTNF3-AMACR	ENST00000382079.3 link	n.689+415G>A		intron_variant	Intron 6 of 8	2		ENSP00000371511.3

Frequencies

GnomAD3 genomes

AF:

0.390

AC:

59299

AN:

151904

Hom.:

11940

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.391

Gnomad AMR

AF:

0.449

Gnomad ASJ

AF:

0.354

Gnomad EAS

AF:

0.486

Gnomad SAS

AF:

0.648

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.360

Gnomad OTH

AF:

0.415

GnomAD4 exome

AF:

0.428

AC:

5585

AN:

13058

Hom.:

1299

Cov.:

AF XY:

0.443

AC XY:

3068

AN XY:

6926

show subpopulations

African (AFR)

AF:

0.410

AC:

AN:

222

American (AMR)

AF:

0.472

AC:

1146

AN:

2428

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

101

AN:

254

East Asian (EAS)

AF:

0.486

AC:

323

AN:

664

South Asian (SAS)

AF:

0.640

AC:

1193

AN:

1864

European-Finnish (FIN)

AF:

0.310

AC:

AN:

200

Middle Eastern (MID)

AF:

0.346

AC:

AN:

European-Non Finnish (NFE)

AF:

0.355

AC:

2452

AN:

6908

Other (OTH)

AF:

0.423

AC:

208

AN:

492

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

140

279

419

558

698

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

180

270

360

450

<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:

0.391

AC:

59369

AN:

152022

Hom.:

11966

Cov.:

AF XY:

0.394

AC XY:

29294

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.396

AC:

16433

AN:

41466

American (AMR)

AF:

0.450

AC:

6880

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.354

AC:

1228

AN:

3468

East Asian (EAS)

AF:

0.486

AC:

2510

AN:

5166

South Asian (SAS)

AF:

0.648

AC:

3124

AN:

4818

European-Finnish (FIN)

AF:

0.317

AC:

3342

AN:

10530

Middle Eastern (MID)

AF:

0.483

AC:

142

AN:

294

European-Non Finnish (NFE)

AF:

0.360

AC:

24467

AN:

67974

Other (OTH)

AF:

0.421

AC:

889

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1875

3750

5626

7501

9376

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

578

1156

1734

2312

2890

<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:

0.376

Hom.:

29948

Bravo

AF:

0.397

Asia WGS

AF:

0.588

AC:

2044

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.2

(source)

DANN

Benign

0.51

PhyloP100

-0.23

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