5-34044302-T-C

Variant names:

• chr5-34044302-T-C
• rs890952
• ENST00000382079.3:n.37-8544A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000382079.3(C1QTNF3-AMACR):​n.37-8544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 152,072 control chromosomes in the GnomAD database, including 33,112 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 0.65 (33112 hom., cov: 32)
• Consequence: C1QTNF3-AMACR ENST00000382079.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 5 publications found

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 (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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QTNF3-AMACR	NR_037951.1	n.112-8544A>G		intron_variant	Intron 1 of 8
C1QTNF3	NR_146599.1	n.895-8544A>G		intron_variant	Intron 7 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF3-AMACR	ENST00000382079.3	n.37-8544A>G		intron_variant	Intron 1 of 8	2		ENSP00000371511.3

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99202 AN: 151954 Hom.: 33092 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.635

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.653 AC: 99260 AN: 152072 Hom.: 33112 Cov.: 32 AF XY: 0.651 AC XY: 48386 AN XY: 74350

African (AFR) AF: 0.532 AC: 22067 AN: 41444

American (AMR) AF: 0.707 AC: 10805 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2360 AN: 3470

East Asian (EAS) AF: 0.869 AC: 4503 AN: 5180

South Asian (SAS) AF: 0.454 AC: 2185 AN: 4818

European-Finnish (FIN) AF: 0.719 AC: 7610 AN: 10588

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47636 AN: 67976

Other (OTH) AF: 0.630 AC: 1328 AN: 2108

Alfa AF: 0.676 Hom.: 12546

Bravo AF: 0.654

Asia WGS AF: 0.609 AC: 2118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.84
PhyloP100		0.079

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

Other links and lift over

dbSNP: rs890952; hg19: chr5-34044407;