rs1029973

Variant names:

• chr4-15437227-C-T
• rs1029973
• NM_031911.5:c.238+1246C>T

Variant summary

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

The NM_031911.5(C1QTNF7):​c.238+1246C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 151,784 control chromosomes in the GnomAD database, including 982 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 0.10 (982 hom., cov: 31)
• Consequence: C1QTNF7 NM_031911.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 5 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031911.5. 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_031911.5	MANE Select	c.238+1246C>T		intron	N/A	NP_114117.1	Q9BXJ2-1
	C1QTNF7	NM_001135170.2		c.259+1246C>T		intron	N/A	NP_001128642.1	Q9BXJ2-2
	C1QTNF7	NM_001135171.2		c.238+1246C>T		intron	N/A	NP_001128643.1	Q9BXJ2-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF7	ENST00000444304.3	TSL:1 MANE Select	c.238+1246C>T		intron	N/A	ENSP00000388914.2	Q9BXJ2-1
	C1QTNF7	ENST00000295297.4	TSL:1	c.259+1246C>T		intron	N/A	ENSP00000295297.4	Q9BXJ2-2
	C1QTNF7	ENST00000429690.5	TSL:4	c.238+1246C>T		intron	N/A	ENSP00000410722.1	Q9BXJ2-1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15624 AN: 151666 Hom.: 978 Cov.: 31

Gnomad AFR AF: 0.0500

Gnomad AMI AF: 0.0485

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0976

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.0966

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.103 AC: 15624 AN: 151784 Hom.: 982 Cov.: 31 AF XY: 0.104 AC XY: 7699 AN XY: 74158

African (AFR) AF: 0.0499 AC: 2066 AN: 41394

American (AMR) AF: 0.111 AC: 1690 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0976 AC: 339 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1576 AN: 5168

South Asian (SAS) AF: 0.0962 AC: 463 AN: 4812

European-Finnish (FIN) AF: 0.138 AC: 1447 AN: 10456

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7683 AN: 67950

Other (OTH) AF: 0.132 AC: 277 AN: 2104

Alfa AF: 0.108 Hom.: 1512

Bravo AF: 0.100

Asia WGS AF: 0.180 AC: 624 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.52
PhyloP100		-0.19
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: rs1029973; hg19: chr4-15438851;