dbSNP rs2295890: NT5E:c.-396G>C (chr6-85449744-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.17

Variant links:

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]

NT5E links:

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ACMG classification

Classification made for transcript

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5E	ENST00000369651 link	c.-396G>C		5_prime_UTR_variant	Exon 1 of 8	2		ENSP00000358665.3		P21589-2

Frequencies

GnomAD3 genomes

AF:

0.184

AC:

28031

AN:

152104

Hom.:

3052

Cov.:

show subpopulations

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.:

AF XY:

0.130

AC XY:

3950

AN XY:

30490

show subpopulations

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.:

AF XY:

0.179

AC XY:

13349

AN XY:

74442

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over