rs2295890

Positions:

• chr6-85449744-G-C

Variant summary

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

The ENST00000369651(NT5E):​c.-396G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 213,556 control chromosomes in the GnomAD database, including 3,697 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 0.18 (3053 hom., cov: 32)
  • Exomes 𝑓: 0.13 (644 hom.)
• Consequence: NT5E ENST00000369651 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

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]

(HGNC:):

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 = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85449744G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5E	ENST00000369651	c.-396G>C		5_prime_UTR_variant	1/8	2		ENSP00000358665.3

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28031 AN: 152104 Hom.: 3052 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0616

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.166

GnomAD4 exome AF: 0.130 AC: 7950 AN: 61332 Hom.: 644 Cov.: 0 AF XY: 0.130 AC XY: 3950 AN XY: 30490

Gnomad4 AFR exome AF: 0.278

Gnomad4 AMR exome AF: 0.0994

Gnomad4 ASJ exome AF: 0.145

Gnomad4 EAS exome AF: 0.0486

Gnomad4 SAS exome AF: 0.151

Gnomad4 FIN exome AF: 0.0915

Gnomad4 NFE exome AF: 0.129

Gnomad4 OTH exome AF: 0.136

GnomAD4 genome AF: 0.184 AC: 28054 AN: 152224 Hom.: 3053 Cov.: 32 AF XY: 0.179 AC XY: 13349 AN XY: 74442

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.0616

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.166

Alfa AF: 0.165 Hom.: 322

Bravo AF: 0.189

Asia WGS AF: 0.116 AC: 403 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	1.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2295890; hg19: chr6-86159462; COSMIC: COSV57629036; COSMIC: COSV57629036;