chr5-34020172-C-T

Position:

• chr5-34020172-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181435.6(C1QTNF3):​c.*411G>A variant causes a 3 prime UTR 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 NM_181435.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.232

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-AMACR (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QTNF3	NM_181435.6	c.*411G>A		3_prime_UTR_variant	6/6	ENST00000382065.8
C1QTNF3-AMACR	NR_037951.1	n.764+415G>A		intron_variant, non_coding_transcript_variant
C1QTNF3	NM_030945.4	c.*411G>A		3_prime_UTR_variant	6/6
C1QTNF3	NR_146599.1	n.1962G>A		non_coding_transcript_exon_variant	12/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1QTNF3	ENST00000382065.8	c.*411G>A		3_prime_UTR_variant	6/6	1	NM_181435.6	P4
C1QTNF3	ENST00000231338.7	c.*411G>A		3_prime_UTR_variant	6/6	1		A1
C1QTNF3	ENST00000513471.5	n.926G>A		non_coding_transcript_exon_variant	3/3	1
C1QTNF3	ENST00000508398.1	n.1081G>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59299 AN: 151904 Hom.: 11940 Cov.: 32

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.: 0 AF XY: 0.443 AC XY: 3068 AN XY: 6926

Gnomad4 AFR exome AF: 0.410

Gnomad4 AMR exome AF: 0.472

Gnomad4 ASJ exome AF: 0.398

Gnomad4 EAS exome AF: 0.486

Gnomad4 SAS exome AF: 0.640

Gnomad4 FIN exome AF: 0.310

Gnomad4 NFE exome AF: 0.355

Gnomad4 OTH exome AF: 0.423

GnomAD4 genome AF: 0.391 AC: 59369 AN: 152022 Hom.: 11966 Cov.: 32 AF XY: 0.394 AC XY: 29294 AN XY: 74314

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.421

Alfa AF: 0.370 Hom.: 17763

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
DANN	Benign	0.51

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

LitVar

Other links and lift over

dbSNP: rs840386; hg19: chr5-34020277;