7-33014502-CT-C

Position:

• chr7-33014502-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001002010.5(NT5C3A):​c.*227delA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.055 (119 hom., cov: 0)
  • Exomes 𝑓: 0.026 (5 hom.)
• Consequence: NT5C3A NM_001002010.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.209

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 -10 ACMG points.

• BP6: Variant 7-33014502-CT-C is Benign according to our data. Variant chr7-33014502-CT-C is described in ClinVar as [Benign]. Clinvar id is 1249936.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5C3A	NM_001002010.5	c.*227delA		3_prime_UTR_variant	9/9	ENST00000610140.7	NP_001002010.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C3A	ENST00000610140	c.*227delA		3_prime_UTR_variant	9/9	1	NM_001002010.5	ENSP00000476480.2

Frequencies

GnomAD3 genomes AF: 0.0551 AC: 3397 AN: 61688 Hom.: 119 Cov.: 0

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.0341

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00230

Gnomad MID AF: 0.0118

Gnomad NFE AF: 0.00313

Gnomad OTH AF: 0.0496

GnomAD3 exomes AF: 0.101 AC: 3936 AN: 38958 Hom.: 3 AF XY: 0.0974 AC XY: 2116 AN XY: 21724

Gnomad AFR exome AF: 0.206

Gnomad AMR exome AF: 0.0917

Gnomad ASJ exome AF: 0.217

Gnomad EAS exome AF: 0.0422

Gnomad SAS exome AF: 0.0521

Gnomad FIN exome AF: 0.178

Gnomad NFE exome AF: 0.102

Gnomad OTH exome AF: 0.110

GnomAD4 exome AF: 0.0259 AC: 9894 AN: 382122 Hom.: 5 Cov.: 3 AF XY: 0.0249 AC XY: 5196 AN XY: 208994

Gnomad4 AFR exome AF: 0.0712

Gnomad4 AMR exome AF: 0.0155

Gnomad4 ASJ exome AF: 0.0719

Gnomad4 EAS exome AF: 0.0248

Gnomad4 SAS exome AF: 0.0110

Gnomad4 FIN exome AF: 0.0193

Gnomad4 NFE exome AF: 0.0255

Gnomad4 OTH exome AF: 0.0325

GnomAD4 genome AF: 0.0553 AC: 3413 AN: 61700 Hom.: 119 Cov.: 0 AF XY: 0.0558 AC XY: 1659 AN XY: 29740

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.0262

Gnomad4 ASJ AF: 0.0341

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00230

Gnomad4 NFE AF: 0.00313

Gnomad4 OTH AF: 0.0488

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 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs78675401; hg19: chr7-33054114;