rs13228827

Variant names:

• chr7-33062902-G-A
• rs13228827
• ENST00000788220.1:n.24G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-33062902-G-A
• chr7-33062902-G-C
• chr7-33062902-G-T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000788220.1(ENSG00000302625):​n.24G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 969,208 control chromosomes in the GnomAD database, including 242,739 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.73 (40222 hom., cov: 33)
  • Exomes 𝑓: 0.70 (202517 hom.)
• Consequence: ENSG00000302625 ENST00000788220.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.438
• Publications: 7 publications found

Genes affected

ENSG00000302625 (HGNC:):

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: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 7-33062902-G-A is Benign according to our data. Variant chr7-33062902-G-A is described in ClinVar as Benign. ClinVar VariationId is 1295988.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788220.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NT5C3A	NM_001002010.5	MANE Select	c.-197C>T		upstream_gene	N/A	NP_001002010.2	X6RM59
	NT5C3A	NM_001374335.1		c.-197C>T		upstream_gene	N/A	NP_001361264.1
	NT5C3A	NM_001002009.3		c.-354C>T		upstream_gene	N/A	NP_001002009.1	Q9H0P0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302625	ENST00000788220.1		n.24G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000302625	ENST00000788224.1		n.24G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000302625	ENST00000788225.1		n.16G>A		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110115 AN: 151860 Hom.: 40175 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.696

GnomAD4 exome AF: 0.702 AC: 573380 AN: 817230 Hom.: 202517 AF XY: 0.698 AC XY: 293330 AN XY: 420454

African (AFR) AF: 0.805 AC: 16150 AN: 20066

American (AMR) AF: 0.799 AC: 24578 AN: 30744

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 10677 AN: 18732

East Asian (EAS) AF: 0.648 AC: 21308 AN: 32872

South Asian (SAS) AF: 0.636 AC: 38618 AN: 60732

European-Finnish (FIN) AF: 0.758 AC: 24235 AN: 31984

Middle Eastern (MID) AF: 0.625 AC: 1794 AN: 2870

European-Non Finnish (NFE) AF: 0.705 AC: 409498 AN: 580552

Other (OTH) AF: 0.686 AC: 26522 AN: 38678

GnomAD4 genome AF: 0.725 AC: 110220 AN: 151978 Hom.: 40222 Cov.: 33 AF XY: 0.727 AC XY: 53975 AN XY: 74292

African (AFR) AF: 0.788 AC: 32645 AN: 41430

American (AMR) AF: 0.748 AC: 11440 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1966 AN: 3464

East Asian (EAS) AF: 0.630 AC: 3234 AN: 5130

South Asian (SAS) AF: 0.623 AC: 3002 AN: 4820

European-Finnish (FIN) AF: 0.760 AC: 8050 AN: 10592

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.703 AC: 47781 AN: 67944

Other (OTH) AF: 0.693 AC: 1463 AN: 2112

Alfa AF: 0.664 Hom.: 2394

Bravo AF: 0.726

Asia WGS AF: 0.628 AC: 2184 AN: 3472

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.89
PhyloP100		-0.44
PromoterAI		0.027	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13228827; hg19: chr7-33102514;