chr7-33021787-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001002010.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NT5C3A	NM_001002010.5	MANE Select	c.354+266A>G		intron	N/A	NP_001002010.2
	NT5C3A	NM_001374335.1		c.255+266A>G		intron	N/A	NP_001361264.1
	NT5C3A	NM_001002009.3		c.252+266A>G		intron	N/A	NP_001002009.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NT5C3A	ENST00000610140.7	TSL:1 MANE Select	c.354+266A>G		intron	N/A	ENSP00000476480.2
	NT5C3A	ENST00000456458.5	TSL:1	n.*259+266A>G		intron	N/A	ENSP00000389676.2
	NT5C3A	ENST00000643244.2		c.252+266A>G		intron	N/A	ENSP00000496364.1

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

African (AFR) AF: 0.763 AC: 6995 AN: 9164

American (AMR) AF: 0.745 AC: 7607 AN: 10212

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 5586 AN: 10144

East Asian (EAS) AF: 0.497 AC: 10446 AN: 21026

South Asian (SAS) AF: 0.611 AC: 20748 AN: 33948

European-Finnish (FIN) AF: 0.752 AC: 13831 AN: 18398

Middle Eastern (MID) AF: 0.607 AC: 835 AN: 1376

European-Non Finnish (NFE) AF: 0.697 AC: 133513 AN: 191658

Other (OTH) AF: 0.677 AC: 12572 AN: 18558

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

African (AFR) AF: 0.770 AC: 31948 AN: 41514

American (AMR) AF: 0.728 AC: 11130 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1942 AN: 3470

East Asian (EAS) AF: 0.488 AC: 2522 AN: 5172

South Asian (SAS) AF: 0.605 AC: 2921 AN: 4826

European-Finnish (FIN) AF: 0.759 AC: 8040 AN: 10592

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47755 AN: 67956

Other (OTH) AF: 0.679 AC: 1432 AN: 2110

Alfa AF: 0.695 Hom.: 10635

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

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.34
PhyloP100		-0.0070
Mutation Taster		=100/0	polymorphism (auto)

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;