ENST00000295297.4:c.14-39454G>A

Variant names:

• chr4-15396282-G-A
• rs1861046
• ENST00000295297.4:c.14-39454G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 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=-0.9).
• 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 rank	MANE	Protein	UniProt
C1QTNF7	NM_001135170.2	c.14-39454G>A		intron_variant	Intron 1 of 2		NP_001128642.1
C1QTNF7	NM_001135171.2	c.-9+21513G>A		intron_variant	Intron 1 of 2		NP_001128643.1
C1QTNF7-AS1	NR_125911.1	n.86+31547C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF7	ENST00000295297.4	c.14-39454G>A		intron_variant	Intron 1 of 2	1		ENSP00000295297.4
C1QTNF7	ENST00000429690.5	c.-9+21513G>A		intron_variant	Intron 1 of 2	4		ENSP00000410722.1
C1QTNF7	ENST00000397700.6	c.14-39454G>A		intron_variant	Intron 2 of 3	4		ENSP00000380812.2

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

African (AFR) AF: 0.201 AC: 8341 AN: 41496

American (AMR) AF: 0.199 AC: 3042 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3470

East Asian (EAS) AF: 0.171 AC: 882 AN: 5158

South Asian (SAS) AF: 0.0768 AC: 371 AN: 4828

European-Finnish (FIN) AF: 0.0653 AC: 693 AN: 10610

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0366 AC: 2488 AN: 68018

Other (OTH) AF: 0.104 AC: 220 AN: 2112

Alfa AF: 0.0625 Hom.: 2039

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
PhyloP100		-0.40
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: rs1861046; hg19: chr4-15397906;