7-33015098-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.895-267G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 151,932 control chromosomes in the GnomAD database, including 40,172 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.72 (40172 hom., cov: 30)
• Consequence: NT5C3A NM_001002010.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.77

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=-0.9).
• BP6: Variant 7-33015098-C-T is Benign according to our data. Variant chr7-33015098-C-T is described in ClinVar as [Benign]. Clinvar id is 1226780.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5C3A	NM_001002010.5	c.895-267G>A		intron_variant		ENST00000610140.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5C3A	ENST00000610140.7	c.895-267G>A		intron_variant		1	NM_001002010.5	P3

Frequencies

GnomAD3 genomes AF: 0.725 AC: 109991 AN: 151814 Hom.: 40123 Cov.: 30

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.696

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.725 AC: 110098 AN: 151932 Hom.: 40172 Cov.: 30 AF XY: 0.726 AC XY: 53893 AN XY: 74228

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.693

Alfa AF: 0.715 Hom.: 5437

Bravo AF: 0.726

Asia WGS AF: 0.626 AC: 2180 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

Nov 12, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.090
Dann	Benign	0.51

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: rs2893457; hg19: chr7-33054710;