7-33015552-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001002010.5(NT5C3A):c.894+118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 655,036 control chromosomes in the GnomAD database, including 177,183 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.76 (44438 hom., cov: 30)
  • Exomes 𝑓: 0.72 (132745 hom.)
• Consequence: NT5C3A NM_001002010.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.08

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 7-33015552-T-C is Benign according to our data. Variant chr7-33015552-T-C is described in ClinVar as [Benign]. Clinvar id is 1253137.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5C3A	NM_001002010.5	c.894+118A>G		intron_variant		ENST00000610140.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5C3A	ENST00000610140.7	c.894+118A>G		intron_variant		1	NM_001002010.5	P3

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115599 AN: 151850 Hom.: 44385 Cov.: 30

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.735

GnomAD4 exome AF: 0.724 AC: 364003 AN: 503068 Hom.: 132745 AF XY: 0.724 AC XY: 193486 AN XY: 267210

Gnomad4 AFR exome AF: 0.852

Gnomad4 AMR exome AF: 0.795

Gnomad4 ASJ exome AF: 0.593

Gnomad4 EAS exome AF: 0.655

Gnomad4 SAS exome AF: 0.749

Gnomad4 FIN exome AF: 0.764

Gnomad4 NFE exome AF: 0.717

Gnomad4 OTH exome AF: 0.722

GnomAD4 genome AF: 0.761 AC: 115709 AN: 151968 Hom.: 44438 Cov.: 30 AF XY: 0.764 AC XY: 56697 AN XY: 74256

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.735

Alfa AF: 0.723 Hom.: 37700

Bravo AF: 0.763

Asia WGS AF: 0.689 AC: 2397 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.22
Dann	Benign	0.38

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

Other links and lift over

dbSNP: rs7790368; hg19: chr7-33055164;