rs9450279

Variant names:

• chr6-85449506-C-T
• rs9450279
• ENST00000369651.7:c.-634C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000369651.7(NT5E):​c.-634C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,122 control chromosomes in the GnomAD database, including 3,360 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 0.19 (3360 hom., cov: 32)
  • Exomes 𝑓: 0.071 (0 hom.)
• Consequence: NT5E ENST00000369651.7 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

NT5E (HGNC:8021): (5'-nucleotidase ecto) The protein encoded by this gene is a plasma membrane protein that catalyzes the conversion of extracellular nucleotides to membrane-permeable nucleosides. The encoded protein is used as a determinant of lymphocyte differentiation. Defects in this gene can lead to the calcification of joints and arteries. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5E	ENST00000369651.7	c.-634C>T		upstream_gene_variant		2		ENSP00000358665.3

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29062 AN: 151962 Hom.: 3359 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0619

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.169

GnomAD4 exome AF: 0.0714 AC: 3 AN: 42 Hom.: 0 AF XY: 0.0909 AC XY: 2 AN XY: 22

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0667

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.191 AC: 29088 AN: 152080 Hom.: 3360 Cov.: 32 AF XY: 0.186 AC XY: 13825 AN XY: 74344

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.0618

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.169

Alfa AF: 0.165 Hom.: 482

Bravo AF: 0.198

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.015
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9450279; hg19: chr6-86159224;