rs7325450

Positions:

• chr13-23892865-A-G
• chr13-23892865-A-T

Variant summary

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

The ENST00000713589.1(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 ENST00000713589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1QTNF9B	NM_001007537.3	c.230-804T>C		intron_variant		ENST00000713589.1	NP_001007538.1
C1QTNF9B	NR_104426.1	n.440-804T>C		intron_variant, non_coding_transcript_variant
C1QTNF9B	XM_047430301.1	c.253-804T>C		intron_variant			XP_047286257.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1QTNF9B	ENST00000713589.1	c.230-804T>C		intron_variant			NM_001007537.3	ENSP00000518885	P1
PCOTH	ENST00000417034.1	n.73+1334A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.370

Alfa AF: 0.374 Hom.: 8435

Bravo AF: 0.398

Asia WGS AF: 0.285 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.78

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: rs7325450; hg19: chr13-24467004;