rs114133078

Variant names:

• chr4-15352761-T-C
• rs114133078
• ENST00000295297.4:c.13+12554T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
C1QTNF7	NM_001135170.2	c.13+12554T>C		intron_variant	Intron 1 of 2		NP_001128642.1
C1QTNF7-AS1	NR_125911.1	n.86+75068A>G		intron_variant	Intron 1 of 5
C1QTNF7	XM_011513772.2	c.13+12554T>C		intron_variant	Intron 2 of 3		XP_011512074.1
C1QTNF7	XM_047449566.1	c.-2614+12554T>C		intron_variant	Intron 1 of 3		XP_047305522.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF7	ENST00000295297.4	c.13+12554T>C		intron_variant	Intron 1 of 2	1		ENSP00000295297.4
C1QTNF7	ENST00000397700.6	c.13+12554T>C		intron_variant	Intron 2 of 3	4		ENSP00000380812.2
C1QTNF7-AS1	ENST00000502344.6	n.86+75068A>G		intron_variant	Intron 1 of 5	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

African (AFR) AF: 0.00739 AC: 307 AN: 41564

American (AMR) AF: 0.0597 AC: 912 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0829 AC: 288 AN: 3472

East Asian (EAS) AF: 0.00194 AC: 10 AN: 5164

South Asian (SAS) AF: 0.0420 AC: 203 AN: 4828

European-Finnish (FIN) AF: 0.0274 AC: 291 AN: 10616

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0313 AC: 2128 AN: 67988

Other (OTH) AF: 0.0308 AC: 65 AN: 2112

Alfa AF: 0.0293 Hom.: 132

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
PhyloP100		0.52
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs114133078; hg19: chr4-15354385;