3-125874014-C-G

Variant names:

• chr3-125874014-C-G
• rs71327718

Variant summary

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

The variant allele was found at a frequency of 0.109 in 152,190 control chromosomes in the GnomAD database, including 993 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 0.11 (993 hom., cov: 32)
• Consequence: ENPP7P4 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 6 publications found

Genes affected

ENPP7P4 (HGNC:48687): (ectonucleotide pyrophosphatase/phosphodiesterase 7 pseudogene 4)

LINC02614 (HGNC:54072): (long intergenic non-protein coding RNA 2614)

ENSG00000284624 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000468859.1. 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
	LINC02614	NR_125395.1		n.292-169G>C		intron	N/A
	LINC02614	NR_125396.1		n.199-169G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02614	ENST00000468859.1	TSL:2	n.1457-10901G>C		intron	N/A
	ENPP7P4	ENST00000487446.1	TSL:6	n.167-8943C>G		intron	N/A
	LINC02614	ENST00000594843.1	TSL:3	n.199-169G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16518 AN: 152072 Hom.: 987 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0827

Gnomad SAS AF: 0.0908

Gnomad FIN AF: 0.0539

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.109 AC: 16537 AN: 152190 Hom.: 993 Cov.: 32 AF XY: 0.107 AC XY: 7956 AN XY: 74402

African (AFR) AF: 0.124 AC: 5136 AN: 41476

American (AMR) AF: 0.120 AC: 1842 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3470

East Asian (EAS) AF: 0.0823 AC: 426 AN: 5174

South Asian (SAS) AF: 0.0894 AC: 431 AN: 4822

European-Finnish (FIN) AF: 0.0539 AC: 572 AN: 10616

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7158 AN: 68008

Other (OTH) AF: 0.139 AC: 295 AN: 2116

Alfa AF: 0.0979 Hom.: 106

Bravo AF: 0.115

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.28

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: rs71327718; hg19: chr3-125592857;