rs3750119

Variant names:

• chr7-33021787-T-A
• rs3750119
• NM_001002010.5:c.354+266A>T

Your query was ambiguous. Multiple possible variants found:

• chr7-33021787-T-A
• chr7-33021787-T-C
• chr7-33021787-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001002010.5(NT5C3A):​c.354+266A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NT5C3A NM_001002010.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 3 publications found

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 Gene-Disease associations (from GenCC):

• hemolytic anemia due to pyrimidine 5' nucleotidase deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet, Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NT5C3A	NM_001002010.5	c.354+266A>T		intron_variant	Intron 4 of 8	ENST00000610140.7	NP_001002010.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5C3A	ENST00000610140.7	c.354+266A>T		intron_variant	Intron 4 of 8	1	NM_001002010.5	ENSP00000476480.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 315394 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 166002

African (AFR) AF: 0.00 AC: 0 AN: 9192

American (AMR) AF: 0.00 AC: 0 AN: 10230

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10184

East Asian (EAS) AF: 0.00 AC: 0 AN: 21096

South Asian (SAS) AF: 0.00 AC: 0 AN: 34026

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 18468

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1380

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 192214

Other (OTH) AF: 0.00 AC: 0 AN: 18604

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 10635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.30
PhyloP100		-0.0070

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

Other links and lift over

dbSNP: rs3750119; hg19: chr7-33061399;