rs71327718

Variant names:

• chr3-125874014-C-G
• rs71327718

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENPP7P4		n.125874014C>G		intragenic_variant
LINC02614	NR_125395.1	n.292-169G>C		intron_variant	Intron 2 of 4
LINC02614	NR_125396.1	n.199-169G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02614	ENST00000468859.1	n.1457-10901G>C		intron_variant	Intron 1 of 1	2
ENPP7P4	ENST00000487446.1	n.167-8943C>G		intron_variant	Intron 1 of 3	6
LINC02614	ENST00000594843.1	n.199-169G>C		intron_variant	Intron 1 of 2	3

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

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0823

Gnomad4 SAS AF: 0.0894

Gnomad4 FIN AF: 0.0539

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.139

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71327718; hg19: chr3-125592857;