rs1861046

Positions:

• chr4-15396282-G-A
• chr4-15396282-G-C

Variant summary

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

The ENST00000295297.4(C1QTNF7):​c.14-39454G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,180 control chromosomes in the GnomAD database, including 1,389 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 (1389 hom., cov: 32)
• Consequence: C1QTNF7 ENST00000295297.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1QTNF7-AS1	NR_125911.1	n.86+31547C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1QTNF7-AS1	ENST00000502344.5	n.86+31547C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000515495.1	n.104+23647C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16124 AN: 152062 Hom.: 1391 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.0778

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.106 AC: 16138 AN: 152180 Hom.: 1389 Cov.: 32 AF XY: 0.110 AC XY: 8177 AN XY: 74426

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.0768

Gnomad4 FIN AF: 0.0653

Gnomad4 NFE AF: 0.0366

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0509 Hom.: 847

Bravo AF: 0.122

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.68

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: rs1861046; hg19: chr4-15397906;