Variant 7-33014500-A-G 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_001002010.5(NT5C3A):c.*230T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 149,234 control chromosomes in the GnomAD database, including 39,891 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.73 ( 39891 hom., cov: 32)

Exomes 𝑓: 0.69 ( 102147 hom. )

Failed GnomAD Quality Control

Consequence

NT5C3A
NM_001002010.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.505

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:

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 7-33014500-A-G is Benign according to our data. Variant chr7-33014500-A-G is described in ClinVar as [Benign]. Clinvar id is 1178214.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5C3A	NM_001002010.5 linkuse as main transcript	c.*230T>C		3_prime_UTR_variant	9/9	ENST00000610140.7	NP_001002010.2	Q9H0P0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C3A	ENST00000610140 linkuse as main transcript	c.*230T>C		3_prime_UTR_variant	9/9	1	NM_001002010.5	ENSP00000476480.2		X6RM59

Frequencies

GnomAD3 genomes

AF:

0.734

AC:

109437

AN:

149112

Hom.:

39841

Cov.:

show subpopulations

Gnomad AFR

AF:

0.807

Gnomad AMI

AF:

0.511

Gnomad AMR

AF:

0.753

Gnomad ASJ

AF:

0.571

Gnomad EAS

AF:

0.643

Gnomad SAS

AF:

0.650

Gnomad FIN

AF:

0.766

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.707

Gnomad OTH

AF:

0.704

GnomAD3 exomes

AF:

0.703

AC:

80312

AN:

114184

Hom.:

28932

AF XY:

0.695

AC XY:

42889

AN XY:

61700

show subpopulations

Gnomad AFR exome

AF:

0.793

Gnomad AMR exome

AF:

0.803

Gnomad ASJ exome

AF:

0.577

Gnomad EAS exome

AF:

0.623

Gnomad SAS exome

AF:

0.635

Gnomad FIN exome

AF:

0.763

Gnomad NFE exome

AF:

0.702

Gnomad OTH exome

AF:

0.689

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.692

AC:

291774

AN:

421842

Hom.:

102147

Cov.:

AF XY:

0.685

AC XY:

158222

AN XY:

231126

show subpopulations

Gnomad4 AFR exome

AF:

0.786

Gnomad4 AMR exome

AF:

0.799

Gnomad4 ASJ exome

AF:

0.570

Gnomad4 EAS exome

AF:

0.645

Gnomad4 SAS exome

AF:

0.629

Gnomad4 FIN exome

AF:

0.757

Gnomad4 NFE exome

AF:

0.696

Gnomad4 OTH exome

AF:

0.687

GnomAD4 genome

AF:

0.734

AC:

109546

AN:

149234

Hom.:

39891

Cov.:

AF XY:

0.736

AC XY:

53615

AN XY:

72822

show subpopulations

Gnomad4 AFR

AF:

0.807

Gnomad4 AMR

AF:

0.753

Gnomad4 ASJ

AF:

0.571

Gnomad4 EAS

AF:

0.643

Gnomad4 SAS

AF:

0.651

Gnomad4 FIN

AF:

0.766

Gnomad4 NFE

AF:

0.707

Gnomad4 OTH

AF:

0.702

Alfa

AF:

0.688

Hom.:

6620

Bravo

AF:

0.726

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

DANN

Benign

0.81

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