NM_031908.6:c.-9-2667A>C

Variant names:

• chr5-160357687-T-G
• rs4585495
• NM_031908.6:c.-9-2667A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031908.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF2	NM_031908.6	MANE Select	c.-9-2667A>C		intron	N/A	NP_114114.3	Q9BXJ5
	C1QTNF2	NM_001366504.1		c.-9-2667A>C		intron	N/A	NP_001353433.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF2	ENST00000652664.2	MANE Select	c.-9-2667A>C		intron	N/A	ENSP00000498651.1	Q9BXJ5
	C1QTNF2	ENST00000393975.4	TSL:1	c.127-2667A>C		intron	N/A	ENSP00000377545.3	A0A499FIM1
	C1QTNF2	ENST00000891629.1		c.-126-2344A>C		intron	N/A	ENSP00000561688.1

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

African (AFR) AF: 0.991 AC: 41192 AN: 41574

American (AMR) AF: 0.957 AC: 14648 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3290 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5176 AN: 5180

South Asian (SAS) AF: 0.967 AC: 4670 AN: 4830

European-Finnish (FIN) AF: 0.952 AC: 10106 AN: 10616

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.946 AC: 64351 AN: 68046

Other (OTH) AF: 0.973 AC: 2054 AN: 2112

Alfa AF: 0.956 Hom.: 22910

Bravo AF: 0.964

Asia WGS AF: 0.990 AC: 3422 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.1
DANN	Benign	0.54
PhyloP100		-0.0060
Mutation Taster		=100/0	polymorphism (auto)

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: rs4585495; hg19: chr5-159784694;