rs213583

Positions:

• chr5-34034708-C-G
• chr5-34034708-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.415+939G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,008 control chromosomes in the GnomAD database, including 17,033 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 0.45 (17033 hom., cov: 32)
• Consequence: C1QTNF3 NM_181435.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1QTNF3	NM_181435.6	c.415+939G>C		intron_variant		ENST00000382065.8	NP_852100.3
C1QTNF3-AMACR	NR_037951.1	n.223+939G>C		intron_variant, non_coding_transcript_variant
C1QTNF3	NM_030945.4	c.196+939G>C		intron_variant			NP_112207.1
C1QTNF3	NR_146599.1	n.1006+939G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1QTNF3	ENST00000382065.8	c.415+939G>C		intron_variant		1	NM_181435.6	ENSP00000371497	P4
C1QTNF3	ENST00000231338.7	c.196+939G>C		intron_variant		1		ENSP00000231338	A1
C1QTNF3	ENST00000508434.1	n.283+939G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68777 AN: 151890 Hom.: 16992 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.453 AC: 68873 AN: 152008 Hom.: 17033 Cov.: 32 AF XY: 0.456 AC XY: 33868 AN XY: 74272

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.501

Alfa AF: 0.394 Hom.: 1536

Bravo AF: 0.467

Asia WGS AF: 0.645 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.25
DANN	Benign	0.75

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: rs213583; hg19: chr5-34034813;