5-160357687-T-G

Position:

• chr5-160357687-T-G

Variant summary

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

The NM_031908.6(C1QTNF2):​c.-9-2667A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 152,340 control chromosomes in the GnomAD database, including 70,536 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 0.96 (70536 hom., cov: 32)
• Consequence: C1QTNF2 NM_031908.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

Genes affected

C1QTNF2 (HGNC:14325): (C1q and TNF related 2) Predicted to enable identical protein binding activity and signaling receptor binding activity. Predicted to be involved in regulation of lipid metabolic process. Predicted to act upstream of or within positive regulation of MAPK cascade; positive regulation of glucose import; and positive regulation of small molecule metabolic process. Predicted to be located in extracellular space. Predicted to be part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1QTNF2	NM_031908.6	c.-9-2667A>C		intron_variant		ENST00000652664.2	NP_114114.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1QTNF2	ENST00000652664.2	c.-9-2667A>C		intron_variant			NM_031908.6	ENSP00000498651	P1
C1QTNF2	ENST00000393975.4	c.127-2667A>C		intron_variant		1		ENSP00000377545

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146452 AN: 152222 Hom.: 70479 Cov.: 32

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.972

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

GnomAD4 genome AF: 0.962 AC: 146568 AN: 152340 Hom.: 70536 Cov.: 32 AF XY: 0.964 AC XY: 71779 AN XY: 74490

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.957

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.952

Gnomad4 NFE AF: 0.946

Gnomad4 OTH AF: 0.973

Alfa AF: 0.950 Hom.: 11334

Bravo AF: 0.964

Asia WGS AF: 0.990 AC: 3422 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.1
DANN	Benign	0.54

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: rs4585495; hg19: chr5-159784694;