rs114133078

chr4-15352761-T-C

Variant summary

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

The ENST00000295297.4(C1QTNF7):c.13+12554T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0288 in 152,234 control chromosomes in the GnomAD database, including 106 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 0.029 (106 hom., cov: 32)
• Consequence: C1QTNF7 ENST00000295297.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.524

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)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1QTNF7-AS1	NR_125911.1	n.86+75068A>G		intron_variant, non_coding_transcript_variant
C1QTNF7	NM_001135170.2	c.13+12554T>C		intron_variant
C1QTNF7	XM_011513772.2	c.13+12554T>C		intron_variant
C1QTNF7	XM_047449566.1	c.-2614+12554T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1QTNF7-AS1	ENST00000502344.5	n.86+75068A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0288 AC: 4386 AN: 152116 Hom.: 107 Cov.: 32

Gnomad AFR AF: 0.00741

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.0594

Gnomad ASJ AF: 0.0829

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.0274

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0313

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0288 AC: 4389 AN: 152234 Hom.: 106 Cov.: 32 AF XY: 0.0289 AC XY: 2153 AN XY: 74432

Gnomad4 AFR AF: 0.00739

Gnomad4 AMR AF: 0.0597

Gnomad4 ASJ AF: 0.0829

Gnomad4 EAS AF: 0.00194

Gnomad4 SAS AF: 0.0420

Gnomad4 FIN AF: 0.0274

Gnomad4 NFE AF: 0.0313

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.0258 Hom.: 8

Bravo AF: 0.0302

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.4
Dann	Benign	0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs114133078; hg19: chr4-15354385;