13-23892865-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001007537.3(C1QTNF9B):​c.230-804T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,234 control chromosomes in the GnomAD database, including 11,210 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 (11210 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001007537.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF9B	NM_001007537.3	MANE Select	c.230-804T>C		intron	N/A	NP_001007538.1
	C1QTNF9B	NR_104426.1		n.440-804T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF9B	ENST00000713589.1	MANE Select	c.230-804T>C		intron	N/A	ENSP00000518885.1
	C1QTNF9B	ENST00000382137.8	TSL:1	c.230-804T>C		intron	N/A	ENSP00000371572.3
	C1QTNF9B	ENST00000382145.5	TSL:1	c.230-804T>C		intron	N/A	ENSP00000371580.1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 58922 AN: 151118 Hom.: 11200 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.330

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.390 AC: 58969 AN: 151234 Hom.: 11210 Cov.: 32 AF XY: 0.387 AC XY: 28569 AN XY: 73856

African (AFR) AF: 0.447 AC: 18477 AN: 41340

American (AMR) AF: 0.339 AC: 5146 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1203 AN: 3448

East Asian (EAS) AF: 0.426 AC: 2167 AN: 5084

South Asian (SAS) AF: 0.215 AC: 1031 AN: 4802

European-Finnish (FIN) AF: 0.393 AC: 4117 AN: 10468

Middle Eastern (MID) AF: 0.328 AC: 95 AN: 290

European-Non Finnish (NFE) AF: 0.378 AC: 25528 AN: 67606

Other (OTH) AF: 0.370 AC: 776 AN: 2098

Alfa AF: 0.376 Hom.: 11592

Bravo AF: 0.398

Asia WGS AF: 0.285 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.78
PhyloP100		-1.3
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: rs7325450; hg19: chr13-24467004;