chr13-23893203-T-C

Position:

• chr13-23893203-T-C

Variant summary

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

The NM_001007537.3(C1QTNF9B):​c.229+936A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,018 control chromosomes in the GnomAD database, including 12,161 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 0.40 (12161 hom., cov: 32)
• Consequence: C1QTNF9B NM_001007537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66

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]

C1QTNF9B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1QTNF9B	NM_001007537.3	c.229+936A>G		intron_variant			NP_001007538.1
C1QTNF9B	XM_047430301.1	c.252+936A>G		intron_variant			XP_047286257.1
C1QTNF9B	NR_104426.1	n.439+936A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1QTNF9B	ENST00000382137.7	c.229+936A>G		intron_variant		1		ENSP00000371572.3
C1QTNF9B	ENST00000382145.5	c.229+936A>G		intron_variant		1		ENSP00000371580.1
C1QTNF9B	ENST00000556521.1	n.430+936A>G		intron_variant		1
PCOTH	ENST00000417034.1	n.73+1672T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60273 AN: 151900 Hom.: 12150 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.397 AC: 60322 AN: 152018 Hom.: 12161 Cov.: 32 AF XY: 0.395 AC XY: 29348 AN XY: 74316

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.377

Alfa AF: 0.384 Hom.: 10275

Bravo AF: 0.399

Asia WGS AF: 0.292 AC: 1018 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	0.014
DANN	Benign	0.18

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7331047; hg19: chr13-24467342;