Variant 7-33015703-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_001002010.5(NT5C3A):c.861G>A(p.Glu287Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00595 in 1,610,512 control chromosomes in the GnomAD database, including 81 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0040 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0061 ( 77 hom. )

Consequence

NT5C3A
NM_001002010.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0450

Variant links:

Genes affected

NT5C3A (HGNC:17820): (5'-nucleotidase, cytosolic IIIA) This gene encodes a member of the 5'-nucleotidase family of enzymes that catalyze the dephosphorylation of nucleoside 5'-monophosphates. The encoded protein is the type 1 isozyme of pyrimidine 5' nucleotidase and catalyzes the dephosphorylation of pyrimidine 5' monophosphates. Mutations in this gene are a cause of hemolytic anemia due to uridine 5-prime monophosphate hydrolase deficiency. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and pseudogenes of this gene are located on the long arm of chromosomes 3 and 4. [provided by RefSeq, Mar 2012]

NT5C3A links:

NT5C3A (HGNC:):

NT5C3A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 7-33015703-C-T is Benign according to our data. Variant chr7-33015703-C-T is described in ClinVar as [Benign]. Clinvar id is 780675.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.045 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00403 (614/152296) while in subpopulation SAS AF= 0.0302 (146/4832). AF 95% confidence interval is 0.0262. There are 4 homozygotes in gnomad4. There are 328 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5C3A	NM_001002010.5 linkuse as main transcript	c.861G>A	p.Glu287Glu	synonymous_variant	8/9	ENST00000610140.7	NP_001002010.2	Q9H0P0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C3A	ENST00000610140.7 linkuse as main transcript	c.861G>A	p.Glu287Glu	synonymous_variant	8/9	1	NM_001002010.5	ENSP00000476480.2		X6RM59

Frequencies

GnomAD3 genomes

AF:

0.00402

AC:

611

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000821

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00491

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0300

Gnomad FIN

AF:

0.00104

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00495

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00671

AC:

1685

AN:

251248

Hom.:

AF XY:

0.00760

AC XY:

1032

AN XY:

135802

show subpopulations

Gnomad AFR exome

AF:

0.000431

Gnomad AMR exome

AF:

0.00608

Gnomad ASJ exome

AF:

0.000695

Gnomad EAS exome

AF:

0.000435

Gnomad SAS exome

AF:

0.0289

Gnomad FIN exome

AF:

0.000647

Gnomad NFE exome

AF:

0.00452

Gnomad OTH exome

AF:

0.00669

GnomAD4 exome

AF:

0.00615

AC:

8965

AN:

1458216

Hom.:

Cov.:

AF XY:

0.00685

AC XY:

4973

AN XY:

725714

show subpopulations

Gnomad4 AFR exome

AF:

0.000838

Gnomad4 AMR exome

AF:

0.00606

Gnomad4 ASJ exome

AF:

0.000651

Gnomad4 EAS exome

AF:

0.000176

Gnomad4 SAS exome

AF:

0.0286

Gnomad4 FIN exome

AF:

0.000711

Gnomad4 NFE exome

AF:

0.00519

Gnomad4 OTH exome

AF:

0.00616

GnomAD4 genome

AF:

0.00403

AC:

614

AN:

152296

Hom.:

Cov.:

AF XY:

0.00440

AC XY:

328

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.000818

Gnomad4 AMR

AF:

0.00490

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.0302

Gnomad4 FIN

AF:

0.00104

Gnomad4 NFE

AF:

0.00495

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00414

Hom.:

Bravo

AF:

0.00329

Asia WGS

AF:

0.0190

AC:

AN:

3478

EpiCase

AF:

0.00453

EpiControl

AF:

0.00415

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

May 25, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 08, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

2.9

DANN

Benign

0.61

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