7-33015529-C-T

Position:

• chr7-33015529-C-T

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+141G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0308 in 632,208 control chromosomes in the GnomAD database, including 652 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.033 (130 hom., cov: 32)
  • Exomes 𝑓: 0.030 (522 hom.)
• Consequence: NT5C3A NM_001002010.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.215

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 7-33015529-C-T is Benign according to our data. Variant chr7-33015529-C-T is described in ClinVar as [Benign]. Clinvar id is 1229434.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5C3A	NM_001002010.5	c.894+141G>A		intron_variant		ENST00000610140.7	NP_001002010.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C3A	ENST00000610140.7	c.894+141G>A		intron_variant		1	NM_001002010.5	ENSP00000476480.2

Frequencies

GnomAD3 genomes AF: 0.0328 AC: 4987 AN: 152070 Hom.: 132 Cov.: 32

Gnomad AFR AF: 0.0540

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.00746

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0203

Gnomad OTH AF: 0.0353

GnomAD4 exome AF: 0.0302 AC: 14485 AN: 480020 Hom.: 522 AF XY: 0.0350 AC XY: 8940 AN XY: 255464

Gnomad4 AFR exome AF: 0.0530

Gnomad4 AMR exome AF: 0.0155

Gnomad4 ASJ exome AF: 0.0403

Gnomad4 EAS exome AF: 0.00821

Gnomad4 SAS exome AF: 0.121

Gnomad4 FIN exome AF: 0.00836

Gnomad4 NFE exome AF: 0.0199

Gnomad4 OTH exome AF: 0.0348

GnomAD4 genome AF: 0.0328 AC: 4989 AN: 152188 Hom.: 130 Cov.: 32 AF XY: 0.0330 AC XY: 2456 AN XY: 74388

Gnomad4 AFR AF: 0.0538

Gnomad4 AMR AF: 0.0238

Gnomad4 ASJ AF: 0.0412

Gnomad4 EAS AF: 0.0186

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.00746

Gnomad4 NFE AF: 0.0203

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0249 Hom.: 5

Bravo AF: 0.0322

Asia WGS AF: 0.0640 AC: 221 AN: 3478

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

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
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

Other links and lift over

dbSNP: rs115931908; hg19: chr7-33055141;