rs7331047

Variant names:

• chr13-23893203-T-C
• rs7331047
• ENST00000382137.8:c.229+936A>G

Variant summary

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

The ENST00000382137.8(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 ENST00000382137.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 2 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=-1.04).
• 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 rank	MANE	Protein	UniProt
C1QTNF9B	NM_001007537.3	c.229+936A>G		intron_variant	Intron 4 of 4		NP_001007538.1
C1QTNF9B	NR_104426.1	n.439+936A>G		intron_variant	Intron 4 of 5
C1QTNF9B	XM_047430301.1	c.252+936A>G		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.229+936A>G		intron_variant	Intron 4 of 4			ENSP00000518885.1

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

African (AFR) AF: 0.449 AC: 18609 AN: 41422

American (AMR) AF: 0.346 AC: 5282 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1235 AN: 3472

East Asian (EAS) AF: 0.453 AC: 2338 AN: 5158

South Asian (SAS) AF: 0.221 AC: 1066 AN: 4818

European-Finnish (FIN) AF: 0.402 AC: 4253 AN: 10576

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.385 AC: 26195 AN: 67970

Other (OTH) AF: 0.377 AC: 798 AN: 2116

Alfa AF: 0.385 Hom.: 12156

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
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7331047; hg19: chr13-24467342;