7-33014505-T-TAAGA

Variant names:

• chr7-33014505-T-TAAGA
• rs199721569
• NM_001002010.5:c.*224_*225insTCTT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001002010.5(NT5C3A):​c.*224_*225insTCTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.75 (39596 hom., cov: 0)
  • Exomes 𝑓: 0.66 (77715 hom.)
  • Failed GnomAD Quality Control
• Consequence: NT5C3A NM_001002010.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.699
• Publications: 2 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: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 7-33014505-T-TAAGA is Benign according to our data. Variant chr7-33014505-T-TAAGA is described in ClinVar as Benign. ClinVar VariationId is 1289594.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NT5C3A	NM_001002010.5	MANE Select	c.*224_*225insTCTT		3_prime_UTR	Exon 9 of 9	NP_001002010.2	X6RM59
	NT5C3A	NM_001374335.1		c.*224_*225insTCTT		3_prime_UTR	Exon 8 of 8	NP_001361264.1
	NT5C3A	NM_001002009.3		c.*224_*225insTCTT		3_prime_UTR	Exon 10 of 10	NP_001002009.1	Q9H0P0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NT5C3A	ENST00000610140.7	TSL:1 MANE Select	c.*224_*225insTCTT		3_prime_UTR	Exon 9 of 9	ENSP00000476480.2	X6RM59
	NT5C3A	ENST00000456458.5	TSL:1	n.*1125_*1126insTCTT		non_coding_transcript_exon	Exon 10 of 10	ENSP00000389676.2	F8WDR0
	NT5C3A	ENST00000456458.5	TSL:1	n.*1125_*1126insTCTT		3_prime_UTR	Exon 10 of 10	ENSP00000389676.2	F8WDR0

Frequencies

GnomAD3 genomes AF: 0.754 AC: 108944 AN: 144406 Hom.: 39553 Cov.: 0

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.729

GnomAD2 exomes AF: 0.612 AC: 51064 AN: 83480 AF XY: 0.602

Gnomad AFR exome AF: 0.720

Gnomad AMR exome AF: 0.709

Gnomad ASJ exome AF: 0.491

Gnomad EAS exome AF: 0.551

Gnomad FIN exome AF: 0.647

Gnomad NFE exome AF: 0.616

Gnomad OTH exome AF: 0.599

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.665 AC: 263928 AN: 396958 Hom.: 77715 Cov.: 6 AF XY: 0.662 AC XY: 142678 AN XY: 215398

African (AFR) AF: 0.731 AC: 8696 AN: 11894

American (AMR) AF: 0.735 AC: 20065 AN: 27300

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 7930 AN: 14330

East Asian (EAS) AF: 0.640 AC: 11278 AN: 17624

South Asian (SAS) AF: 0.652 AC: 33106 AN: 50802

European-Finnish (FIN) AF: 0.708 AC: 12203 AN: 17240

Middle Eastern (MID) AF: 0.611 AC: 996 AN: 1630

European-Non Finnish (NFE) AF: 0.663 AC: 156105 AN: 235488

Other (OTH) AF: 0.656 AC: 13549 AN: 20650

GnomAD4 genome AF: 0.755 AC: 109043 AN: 144518 Hom.: 39596 Cov.: 0 AF XY: 0.756 AC XY: 53338 AN XY: 70546

African (AFR) AF: 0.811 AC: 32301 AN: 39844

American (AMR) AF: 0.769 AC: 11270 AN: 14650

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 1960 AN: 3274

East Asian (EAS) AF: 0.691 AC: 3189 AN: 4612

South Asian (SAS) AF: 0.709 AC: 2979 AN: 4200

European-Finnish (FIN) AF: 0.776 AC: 7836 AN: 10094

Middle Eastern (MID) AF: 0.712 AC: 178 AN: 250

European-Non Finnish (NFE) AF: 0.732 AC: 47419 AN: 64788

Other (OTH) AF: 0.729 AC: 1456 AN: 1998

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.725

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
PhyloP100		0.70
Mutation Taster		=2/98	disease causing

Splicing

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

Other links and lift over

dbSNP: rs199721569; hg19: chr7-33054117; COSMIC: COSV54237302; COSMIC: COSV54237302;