rs7663443

Variant names:

• chr4-15307070-T-C
• rs7663443
• ENST00000502344.6:n.87-43606A>G

Variant summary

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

The ENST00000502344.6(C1QTNF7-AS1):​n.87-43606A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 152,290 control chromosomes in the GnomAD database, including 873 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 0.067 (873 hom., cov: 33)
• Consequence: C1QTNF7-AS1 ENST00000502344.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 1 publications found

Genes affected

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502344.6. 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-AS1	NR_125911.1		n.87-43606A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF7-AS1	ENST00000502344.6	TSL:3	n.87-43606A>G		intron	N/A
	C1QTNF7-AS1	ENST00000803075.1		n.88-7414A>G		intron	N/A
	C1QTNF7-AS1	ENST00000803076.1		n.191-7414A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0673 AC: 10239 AN: 152172 Hom.: 875 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0289

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0553

Gnomad FIN AF: 0.00781

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0501

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

GnomAD4 genome AF: 0.0673 AC: 10249 AN: 152290 Hom.: 873 Cov.: 33 AF XY: 0.0652 AC XY: 4855 AN XY: 74466

African (AFR) AF: 0.202 AC: 8380 AN: 41532

American (AMR) AF: 0.0289 AC: 442 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0555 AC: 268 AN: 4826

European-Finnish (FIN) AF: 0.00781 AC: 83 AN: 10626

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0132 AC: 901 AN: 68028

Other (OTH) AF: 0.0506 AC: 107 AN: 2116

Alfa AF: 0.0224 Hom.: 200

Bravo AF: 0.0739

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.49
PhyloP100		0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7663443;

hg19: chr4-15308694;