rs16891867

Positions:

• chr4-15395740-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001135170.2(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 NM_001135170.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

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:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
C1QTNF7	NM_001135170.2	c.14-39996A>G		intron_variant			NP_001128642.1
C1QTNF7	NM_001135171.2	c.-9+20971A>G		intron_variant			NP_001128643.1
C1QTNF7	XM_011513772.2	c.14-39996A>G		intron_variant			XP_011512074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1QTNF7	ENST00000295297.4	c.14-39996A>G		intron_variant		1		ENSP00000295297.4
C1QTNF7	ENST00000429690.5	c.-9+20971A>G		intron_variant		4		ENSP00000410722.1
C1QTNF7	ENST00000397700.6	c.14-39996A>G		intron_variant		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

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.0766

Gnomad4 FIN AF: 0.0652

Gnomad4 NFE AF: 0.0366

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0502 Hom.: 463

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs16891867; hg19: chr4-15397364;