Variant 6-85489611-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_002526.4(NT5E):c.1210+12G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 1,585,018 control chromosomes in the GnomAD database, including 267,018 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 23113 hom., cov: 32)

Exomes 𝑓: 0.58 ( 243905 hom. )

Consequence

NT5E
NM_002526.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:3

Conservation

PhyloP100: -1.13

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 6-85489611-G-C is Benign according to our data. Variant chr6-85489611-G-C is described in ClinVar as [Benign]. Clinvar id is 1174653.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-85489611-G-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5E	NM_002526.4 link	c.1210+12G>C		intron_variant		ENST00000257770.8	NP_002517.1	P21589-1Q6NZX3
NT5E	NM_001204813.2 link	c.1210+12G>C		intron_variant			NP_001191742.1	P21589-2Q6NZX3

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
NT5E	ENST00000257770.8 link	c.1210+12G>C	intron_variant	1	NM_002526.4	ENSP00000257770.3	P21589-1
NT5E	ENST00000369651.7 link	c.1210+12G>C	intron_variant	2		ENSP00000358665.3	P21589-2
NT5E	ENST00000416334.5 link	c.502+12G>C	intron_variant	3		ENSP00000414674.1	H0Y7R7
NT5E	ENST00000437581.1 link	c.295+12G>C	intron_variant	3		ENSP00000387630.1	H0Y3X5

Frequencies

GnomAD3 genomes

AF:

0.542

AC:

82354

AN:

151852

Hom.:

23093

Cov.:

show subpopulations

Gnomad AFR

AF:

0.404

Gnomad AMI

AF:

0.713

Gnomad AMR

AF:

0.685

Gnomad ASJ

AF:

0.632

Gnomad EAS

AF:

0.549

Gnomad SAS

AF:

0.708

Gnomad FIN

AF:

0.542

Gnomad MID

AF:

0.694

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.572

GnomAD3 exomes

AF:

0.606

AC:

149958

AN:

247272

Hom.:

46899

AF XY:

0.610

AC XY:

81485

AN XY:

133522

show subpopulations

Gnomad AFR exome

AF:

0.402

Gnomad AMR exome

AF:

0.790

Gnomad ASJ exome

AF:

0.638

Gnomad EAS exome

AF:

0.528

Gnomad SAS exome

AF:

0.719

Gnomad FIN exome

AF:

0.534

Gnomad NFE exome

AF:

0.572

Gnomad OTH exome

AF:

0.609

GnomAD4 exome

AF:

0.580

AC:

830558

AN:

1433048

Hom.:

243905

Cov.:

AF XY:

0.584

AC XY:

416957

AN XY:

714368

show subpopulations

Gnomad4 AFR exome

AF:

0.398

Gnomad4 AMR exome

AF:

0.777

Gnomad4 ASJ exome

AF:

0.632

Gnomad4 EAS exome

AF:

0.553

Gnomad4 SAS exome

AF:

0.721

Gnomad4 FIN exome

AF:

0.536

Gnomad4 NFE exome

AF:

0.567

Gnomad4 OTH exome

AF:

0.585

GnomAD4 genome

AF:

0.542

AC:

82412

AN:

151970

Hom.:

23113

Cov.:

AF XY:

0.548

AC XY:

40667

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.403

Gnomad4 AMR

AF:

0.686

Gnomad4 ASJ

AF:

0.632

Gnomad4 EAS

AF:

0.549

Gnomad4 SAS

AF:

0.709

Gnomad4 FIN

AF:

0.542

Gnomad4 NFE

AF:

0.574

Gnomad4 OTH

AF:

0.575

Alfa

AF:

0.514

Hom.:

2832

Bravo

AF:

0.547

Asia WGS

AF:

0.636

AC:

2211

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Hereditary arterial and articular multiple calcification syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.30

DANN

Benign

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over