ENST00000502344.6:n.154+7533A>G

Variant names:

• chr4-15255864-T-C
• rs10027043
• ENST00000502344.6:n.154+7533A>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.154+7533A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,074 control chromosomes in the GnomAD database, including 38,506 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 0.70 (38506 hom., cov: 31)
• Consequence: C1QTNF7-AS1 ENST00000502344.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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.154+7533A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF7-AS1	ENST00000502344.6	TSL:3	n.154+7533A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106538 AN: 151956 Hom.: 38436 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.701 AC: 106667 AN: 152074 Hom.: 38506 Cov.: 31 AF XY: 0.709 AC XY: 52684 AN XY: 74332

African (AFR) AF: 0.838 AC: 34770 AN: 41490

American (AMR) AF: 0.702 AC: 10740 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2040 AN: 3466

East Asian (EAS) AF: 0.994 AC: 5149 AN: 5178

South Asian (SAS) AF: 0.744 AC: 3591 AN: 4824

European-Finnish (FIN) AF: 0.725 AC: 7643 AN: 10542

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40525 AN: 67966

Other (OTH) AF: 0.664 AC: 1402 AN: 2112

Alfa AF: 0.645 Hom.: 24700

Bravo AF: 0.706

Asia WGS AF: 0.869 AC: 3017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.3
DANN	Benign	0.77
PhyloP100		0.37

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: rs10027043;

hg19: chr4-15257488;