rs16891867

Variant names:

• chr4-15395740-A-G
• rs16891867
• ENST00000295297.4:c.14-39996A>G

Variant summary

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

The ENST00000295297.4(C1QTNF7):​c.14-39996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,192 control chromosomes in the GnomAD database, including 1,423 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 (1423 hom., cov: 32)
• Consequence: C1QTNF7 ENST00000295297.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 15 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 = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1QTNF7	NM_001135170.2	c.14-39996A>G		intron_variant	Intron 1 of 2		NP_001128642.1
C1QTNF7	NM_001135171.2	c.-9+20971A>G		intron_variant	Intron 1 of 2		NP_001128643.1
C1QTNF7-AS1	NR_125911.1	n.86+32089T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1QTNF7	ENST00000295297.4	c.14-39996A>G		intron_variant	Intron 1 of 2	1		ENSP00000295297.4
C1QTNF7	ENST00000429690.5	c.-9+20971A>G		intron_variant	Intron 1 of 2	4		ENSP00000410722.1
C1QTNF7	ENST00000397700.6	c.14-39996A>G		intron_variant	Intron 2 of 3	4		ENSP00000380812.2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16305 AN: 152074 Hom.: 1425 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.0652

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.107 AC: 16320 AN: 152192 Hom.: 1423 Cov.: 32 AF XY: 0.111 AC XY: 8240 AN XY: 74414

African (AFR) AF: 0.206 AC: 8527 AN: 41492

American (AMR) AF: 0.198 AC: 3032 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3468

East Asian (EAS) AF: 0.171 AC: 884 AN: 5168

South Asian (SAS) AF: 0.0766 AC: 370 AN: 4828

European-Finnish (FIN) AF: 0.0652 AC: 692 AN: 10614

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

European-Non Finnish (NFE) AF: 0.0366 AC: 2490 AN: 68024

Other (OTH) AF: 0.106 AC: 224 AN: 2116

Alfa AF: 0.0618 Hom.: 1869

Bravo AF: 0.124

Asia WGS AF: 0.139 AC: 482 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	2.0
DANN	Benign	0.57
PhyloP100		-0.20
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: rs16891867; hg19: chr4-15397364;