4-15284998-A-G

Variant names:

• chr4-15284998-A-G
• rs6449123
• ENST00000502344.6:n.87-21534T>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.87-21534T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 150,870 control chromosomes in the GnomAD database, including 38,403 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 (38403 hom., cov: 32)
• Consequence: C1QTNF7-AS1 ENST00000502344.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• 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=-1.04).
• 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.87-21534T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1QTNF7-AS1	ENST00000502344.6	TSL:3	n.87-21534T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.702 AC: 105928 AN: 150788 Hom.: 38345 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.703 AC: 106028 AN: 150870 Hom.: 38403 Cov.: 32 AF XY: 0.710 AC XY: 52351 AN XY: 73718

African (AFR) AF: 0.844 AC: 34861 AN: 41322

American (AMR) AF: 0.702 AC: 10639 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2037 AN: 3464

East Asian (EAS) AF: 0.995 AC: 5135 AN: 5162

South Asian (SAS) AF: 0.747 AC: 3583 AN: 4796

European-Finnish (FIN) AF: 0.725 AC: 7260 AN: 10014

Middle Eastern (MID) AF: 0.486 AC: 139 AN: 286

European-Non Finnish (NFE) AF: 0.596 AC: 40320 AN: 67650

Other (OTH) AF: 0.663 AC: 1392 AN: 2100

Alfa AF: 0.678 Hom.: 4609

Bravo AF: 0.708

Asia WGS AF: 0.868 AC: 2936 AN: 3386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.29
PhyloP100		-2.1

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: rs6449123;

hg19: chr4-15286622;