4-15390935-T-C

Position:

• chr4-15390935-T-C

Variant summary

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

The NM_001135170.2(C1QTNF7):​c.14-44801T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,802 control chromosomes in the GnomAD database, including 18,803 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 0.48 (18803 hom., cov: 31)
• Consequence: C1QTNF7 NM_001135170.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

Genes affected

C1QTNF7 (HGNC:14342): (C1q and TNF related 7) Predicted to enable identical protein binding activity. Predicted to be located in extracellular space. Predicted to be part of collagen trimer. [provided by Alliance of Genome Resources, Apr 2022]

C1QTNF7-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1QTNF7	NM_001135170.2	c.14-44801T>C		intron_variant			NP_001128642.1
C1QTNF7	NM_001135171.2	c.-9+16166T>C		intron_variant			NP_001128643.1
C1QTNF7	XM_011513772.2	c.14-44801T>C		intron_variant			XP_011512074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1QTNF7	ENST00000295297.4	c.14-44801T>C		intron_variant		1		ENSP00000295297.4
C1QTNF7	ENST00000429690.5	c.-9+16166T>C		intron_variant		4		ENSP00000410722.1
C1QTNF7	ENST00000397700.6	c.14-44801T>C		intron_variant		4		ENSP00000380812.2

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72473 AN: 151686 Hom.: 18772 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.478 AC: 72559 AN: 151802 Hom.: 18803 Cov.: 31 AF XY: 0.482 AC XY: 35743 AN XY: 74154

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.412

Alfa AF: 0.397 Hom.: 5825

Bravo AF: 0.494

Asia WGS AF: 0.490 AC: 1703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.55

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: rs4575989; hg19: chr4-15392559;