4-15334809-A-G

Variant names:

• chr4-15334809-A-G
• rs6449126
• ENST00000502344.6:n.87-71345T>C

Variant summary

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

The ENST00000502344.6(C1QTNF7-AS1):​n.87-71345T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,048 control chromosomes in the GnomAD database, including 25,249 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 0.57 (25249 hom., cov: 32)
• Consequence: C1QTNF7-AS1 ENST00000502344.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400
• 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=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF7-AS1	NR_125911.1		n.87-71345T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF7-AS1	ENST00000502344.6	TSL:3	n.87-71345T>C		intron	N/A
	C1QTNF7-AS1	ENST00000803075.1		n.88-35153T>C		intron	N/A
	C1QTNF7-AS1	ENST00000803076.1		n.190+2102T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86508 AN: 151930 Hom.: 25222 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.569 AC: 86587 AN: 152048 Hom.: 25249 Cov.: 32 AF XY: 0.572 AC XY: 42518 AN XY: 74298

African (AFR) AF: 0.678 AC: 28118 AN: 41476

American (AMR) AF: 0.458 AC: 6995 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1854 AN: 3470

East Asian (EAS) AF: 0.726 AC: 3748 AN: 5160

South Asian (SAS) AF: 0.524 AC: 2526 AN: 4822

European-Finnish (FIN) AF: 0.630 AC: 6647 AN: 10544

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34964 AN: 67982

Other (OTH) AF: 0.534 AC: 1127 AN: 2112

Alfa AF: 0.469 Hom.: 2045

Bravo AF: 0.560

Asia WGS AF: 0.607 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	9.5
DANN	Benign	0.78
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs6449126; hg19: chr4-15336433;