rs4698107

Positions:

• chr4-15412388-G-A
• chr4-15412388-G-T

Variant summary

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

The ENST00000295297.4(C1QTNF7):​c.14-23348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 149,380 control chromosomes in the GnomAD database, including 1,339 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 0.11 (1339 hom., cov: 30)
• Consequence: C1QTNF7 ENST00000295297.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76

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:40683): (C1QTNF7 antisense RNA 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QTNF7-AS1	NR_125911.1	n.86+15441C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1QTNF7-AS1	ENST00000502344.5	n.86+15441C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000515495.1	n.104+7541C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16090 AN: 149268 Hom.: 1339 Cov.: 30

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0780

Gnomad FIN AF: 0.0674

Gnomad MID AF: 0.0294

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.108 AC: 16111 AN: 149380 Hom.: 1339 Cov.: 30 AF XY: 0.112 AC XY: 8152 AN XY: 72716

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.0770

Gnomad4 FIN AF: 0.0674

Gnomad4 NFE AF: 0.0375

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0384 Hom.: 46

Bravo AF: 0.124

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.33

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: rs4698107; hg19: chr4-15414012;