rs10230500

chr7-33041406-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001002010.5(NT5C3A):c.139-14491A>G 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 152,066 control chromosomes in the GnomAD database, including 40,205 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (40205 hom., cov: 31)
• Consequence: NT5C3A NM_001002010.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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.139-14491A>G		intron_variant		ENST00000610140.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5C3A	ENST00000610140.7	c.139-14491A>G		intron_variant		1	NM_001002010.5	P3
NT5C3A	ENST00000456458.5	c.154-5418A>G		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110095 AN: 151948 Hom.: 40156 Cov.: 31

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.703

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: 110202 AN: 152066 Hom.: 40205 Cov.: 31 AF XY: 0.726 AC XY: 53964 AN XY: 74316

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.693

Alfa AF: 0.695 Hom.: 61820

Bravo AF: 0.726

Asia WGS AF: 0.626 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.51
Dann	Benign	0.47

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: rs10230500; hg19: chr7-33081018;