13-23892865-A-T

Variant names:

• chr13-23892865-A-T
• rs7325450
• NM_001007537.3:c.230-804T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001007537.3(C1QTNF9B):​c.230-804T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: C1QTNF9B NM_001007537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 3 publications found

Genes affected

C1QTNF9B (HGNC:34072): (C1q and TNF related 9B) Predicted to enable hormone activity and identical protein binding activity. Predicted to act upstream of or within several processes, including energy homeostasis; negative regulation of cell size; and positive regulation of protein serine/threonine kinase activity. Predicted to be located in extracellular space. Predicted to be part of collagen trimer. [provided by Alliance of Genome Resources, Apr 2022]

PCOTH (HGNC:39839): (prostate and testis expressed opposite C1QTNF9B and MIPEP) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QTNF9B	NM_001007537.3	c.230-804T>A		intron_variant	Intron 4 of 4	ENST00000713589.1	NP_001007538.1
C1QTNF9B	NR_104426.1	n.440-804T>A		intron_variant	Intron 4 of 5
C1QTNF9B	XM_047430301.1	c.253-804T>A		intron_variant	Intron 3 of 4		XP_047286257.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF9B	ENST00000713589.1	c.230-804T>A		intron_variant	Intron 4 of 4		NM_001007537.3	ENSP00000518885.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.54
DANN	Benign	0.81
PhyloP100		-1.3

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: rs7325450; hg19: chr13-24467004;