dbSNP rs890950: C1QTNF3-AMACR:n.37-8202C>T (chr5-34043960-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000382079.3(C1QTNF3-AMACR):n.37-8202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,068 control chromosomes in the GnomAD database, including 5,022 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 0.25 ( 5019 hom., cov: 32)

Exomes 𝑓: 0.33 ( 3 hom. )

Consequence

C1QTNF3-AMACR
ENST00000382079.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.96

Publications

3 publications found

Variant links:

Genes affected

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:

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:

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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=-1.07).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000382079.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF3-AMACR	NR_037951.1		n.112-8202C>T		intron	N/A
	C1QTNF3	NR_146599.1		n.895-8202C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF3-AMACR	ENST00000382079.3	TSL:2	n.37-8202C>T		intron	N/A	ENSP00000371511.3	E9PGA6

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37294

AN:

151920

Hom.:

5005

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.307

Gnomad EAS

AF:

0.112

Gnomad SAS

AF:

0.449

Gnomad FIN

AF:

0.279

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.288

Gnomad OTH

AF:

0.284

GnomAD4 exome

AF:

0.333

AC:

AN:

Hom.:

AF XY:

0.346

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.350

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.245

AC:

37315

AN:

152038

Hom.:

5019

Cov.:

AF XY:

0.249

AC XY:

18521

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.145

AC:

6031

AN:

41470

American (AMR)

AF:

0.257

AC:

3921

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.307

AC:

1064

AN:

3468

East Asian (EAS)

AF:

0.112

AC:

576

AN:

5160

South Asian (SAS)

AF:

0.449

AC:

2164

AN:

4816

European-Finnish (FIN)

AF:

0.279

AC:

2951

AN:

10560

Middle Eastern (MID)

AF:

0.425

AC:

125

AN:

294

European-Non Finnish (NFE)

AF:

0.288

AC:

19579

AN:

67960

Other (OTH)

AF:

0.288

AC:

609

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1397

2793

4190

5586

6983

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

392

784

1176

1568

1960

<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:

0.262

Hom.:

732

Bravo

AF:

0.234

Asia WGS

AF:

0.318

AC:

1104

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.79

(source)

DANN

Benign

0.54

PhyloP100

-3.0

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over