4-15419399-C-T

Variant names:

• chr4-15419399-C-T
• rs1990525
• ENST00000295297.4:c.14-16337C>T

Variant summary

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

The NM_001135170.2(C1QTNF7):​c.14-16337C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.948 in 152,306 control chromosomes in the GnomAD database, including 68,478 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 0.95 (68478 hom., cov: 32)
• Consequence: C1QTNF7 NM_001135170.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135170.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF7	NM_001135170.2		c.14-16337C>T		intron	N/A	NP_001128642.1	Q9BXJ2-2
	C1QTNF7	NM_001135171.2		c.-8-16337C>T		intron	N/A	NP_001128643.1	Q9BXJ2-1
	C1QTNF7-AS1	NR_125911.1		n.86+8430G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF7	ENST00000295297.4	TSL:1	c.14-16337C>T		intron	N/A	ENSP00000295297.4	Q9BXJ2-2
	C1QTNF7	ENST00000429690.5	TSL:4	c.-8-16337C>T		intron	N/A	ENSP00000410722.1	Q9BXJ2-1
	C1QTNF7	ENST00000397700.6	TSL:4	c.14-16337C>T		intron	N/A	ENSP00000380812.2	A0A0A0MS83

Frequencies

GnomAD3 genomes AF: 0.948 AC: 144216 AN: 152188 Hom.: 68410 Cov.: 32

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.985

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.948 AC: 144343 AN: 152306 Hom.: 68478 Cov.: 32 AF XY: 0.949 AC XY: 70715 AN XY: 74478

African (AFR) AF: 0.982 AC: 40835 AN: 41570

American (AMR) AF: 0.942 AC: 14405 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3157 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5175 AN: 5176

South Asian (SAS) AF: 0.985 AC: 4753 AN: 4824

European-Finnish (FIN) AF: 0.946 AC: 10038 AN: 10612

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.924 AC: 62834 AN: 68038

Other (OTH) AF: 0.938 AC: 1982 AN: 2112

Alfa AF: 0.935 Hom.: 42245

Bravo AF: 0.948

Asia WGS AF: 0.992 AC: 3448 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.8
DANN	Benign	0.55
PhyloP100		0.33
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: rs1990525; hg19: chr4-15421023;