5-34053516-T-C

Variant names:

• chr5-34053516-T-C
• rs7379110
• ENST00000382079.3:n.37-17758A>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.37-17758A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,032 control chromosomes in the GnomAD database, including 25,934 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 0.57 (25934 hom., cov: 32)
• Consequence: C1QTNF3-AMACR ENST00000382079.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.894
• Publications: 4 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]

ENSG00000290548 (HGNC:):

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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QTNF3-AMACR	NR_037951.1	n.112-17758A>G		intron_variant	Intron 1 of 8
C1QTNF3	NR_146599.1	n.895-17758A>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.37-17758A>G		intron_variant	Intron 1 of 8	2		ENSP00000371511.3
ENSG00000290548	ENST00000828990.1	n.587-1406A>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85900 AN: 151914 Hom.: 25922 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.565 AC: 85934 AN: 152032 Hom.: 25934 Cov.: 32 AF XY: 0.564 AC XY: 41933 AN XY: 74332

African (AFR) AF: 0.355 AC: 14701 AN: 41454

American (AMR) AF: 0.636 AC: 9727 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2107 AN: 3472

East Asian (EAS) AF: 0.846 AC: 4368 AN: 5164

South Asian (SAS) AF: 0.340 AC: 1642 AN: 4824

European-Finnish (FIN) AF: 0.692 AC: 7310 AN: 10562

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.651 AC: 44247 AN: 67956

Other (OTH) AF: 0.541 AC: 1144 AN: 2114

Alfa AF: 0.622 Hom.: 128336

Bravo AF: 0.563

Asia WGS AF: 0.554 AC: 1926 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.6
DANN	Benign	0.82
PhyloP100		0.89

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: rs7379110; hg19: chr5-34053621;