4-15390935-T-C

Variant names:

• chr4-15390935-T-C
• rs4575989
• ENST00000295297.4:c.14-44801T>C

Variant summary

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

The ENST00000295297.4(C1QTNF7):​c.14-44801T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,802 control chromosomes in the GnomAD database, including 18,803 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 (18803 hom., cov: 31)
• Consequence: C1QTNF7 ENST00000295297.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QTNF7	NM_001135170.2	c.14-44801T>C		intron_variant	Intron 1 of 2		NP_001128642.1
C1QTNF7	NM_001135171.2	c.-9+16166T>C		intron_variant	Intron 1 of 2		NP_001128643.1
C1QTNF7-AS1	NR_125911.1	n.86+36894A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF7	ENST00000295297.4	c.14-44801T>C		intron_variant	Intron 1 of 2	1		ENSP00000295297.4
C1QTNF7	ENST00000429690.5	c.-9+16166T>C		intron_variant	Intron 1 of 2	4		ENSP00000410722.1
C1QTNF7	ENST00000397700.6	c.14-44801T>C		intron_variant	Intron 2 of 3	4		ENSP00000380812.2

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72473 AN: 151686 Hom.: 18772 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.478 AC: 72559 AN: 151802 Hom.: 18803 Cov.: 31 AF XY: 0.482 AC XY: 35743 AN XY: 74154

African (AFR) AF: 0.677 AC: 28051 AN: 41408

American (AMR) AF: 0.525 AC: 8012 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1283 AN: 3468

East Asian (EAS) AF: 0.495 AC: 2535 AN: 5120

South Asian (SAS) AF: 0.462 AC: 2215 AN: 4796

European-Finnish (FIN) AF: 0.405 AC: 4256 AN: 10504

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24682 AN: 67934

Other (OTH) AF: 0.412 AC: 868 AN: 2106

Alfa AF: 0.398 Hom.: 6563

Bravo AF: 0.494

Asia WGS AF: 0.490 AC: 1703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.55
PhyloP100		-2.3
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: rs4575989; hg19: chr4-15392559;