7-33021787-T-C

Position:

• chr7-33021787-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.354+266A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 466,606 control chromosomes in the GnomAD database, including 111,550 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.71 (38931 hom., cov: 33)
  • Exomes 𝑓: 0.67 (72619 hom.)
• Consequence: NT5C3A NM_001002010.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.00700

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=-0.91).
• BP6: Variant 7-33021787-T-C is Benign according to our data. Variant chr7-33021787-T-C is described in ClinVar as [Benign]. Clinvar id is 1230632.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5C3A	NM_001002010.5	c.354+266A>G		intron_variant		ENST00000610140.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5C3A	ENST00000610140.7	c.354+266A>G		intron_variant		1	NM_001002010.5	P3

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108233 AN: 152004 Hom.: 38892 Cov.: 33

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.684

GnomAD4 exome AF: 0.675 AC: 212133 AN: 314484 Hom.: 72619 Cov.: 2 AF XY: 0.669 AC XY: 110743 AN XY: 165516

Gnomad4 AFR exome AF: 0.763

Gnomad4 AMR exome AF: 0.745

Gnomad4 ASJ exome AF: 0.551

Gnomad4 EAS exome AF: 0.497

Gnomad4 SAS exome AF: 0.611

Gnomad4 FIN exome AF: 0.752

Gnomad4 NFE exome AF: 0.697

Gnomad4 OTH exome AF: 0.677

GnomAD4 genome AF: 0.712 AC: 108328 AN: 152122 Hom.: 38931 Cov.: 33 AF XY: 0.713 AC XY: 53001 AN XY: 74370

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.679

Alfa AF: 0.711 Hom.: 4556

Bravo AF: 0.712

Asia WGS AF: 0.546 AC: 1898 AN: 3470

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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.34

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: rs3750119; hg19: chr7-33061399;