rs4629443

Variant names:

• chr4-15384242-C-T
• rs4629443
• ENST00000295297.4:c.13+44035C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000295297.4(C1QTNF7):​c.13+44035C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,086 control chromosomes in the GnomAD database, including 19,166 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 (19166 hom., cov: 32)
• Consequence: C1QTNF7 ENST00000295297.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QTNF7	NM_001135170.2	c.13+44035C>T		intron_variant	Intron 1 of 2		NP_001128642.1
C1QTNF7	NM_001135171.2	c.-9+9473C>T		intron_variant	Intron 1 of 2		NP_001128643.1
C1QTNF7-AS1	NR_125911.1	n.86+43587G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF7	ENST00000295297.4	c.13+44035C>T		intron_variant	Intron 1 of 2	1		ENSP00000295297.4
C1QTNF7	ENST00000429690.5	c.-9+9473C>T		intron_variant	Intron 1 of 2	4		ENSP00000410722.1
C1QTNF7	ENST00000397700.6	c.13+44035C>T		intron_variant	Intron 2 of 3	4		ENSP00000380812.2

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72946 AN: 151968 Hom.: 19133 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.480 AC: 73034 AN: 152086 Hom.: 19166 Cov.: 32 AF XY: 0.484 AC XY: 35971 AN XY: 74330

African (AFR) AF: 0.691 AC: 28679 AN: 41490

American (AMR) AF: 0.525 AC: 8020 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1281 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2548 AN: 5184

South Asian (SAS) AF: 0.461 AC: 2223 AN: 4818

European-Finnish (FIN) AF: 0.401 AC: 4246 AN: 10580

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24505 AN: 67948

Other (OTH) AF: 0.415 AC: 876 AN: 2110

Alfa AF: 0.399 Hom.: 6773

Bravo AF: 0.497

Asia WGS AF: 0.488 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		-0.63
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4629443; hg19: chr4-15385866;