7-33014505-T-TAAGA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.699
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NT5C3ANM_001002010.5 linkuse as main transcriptc.*224_*225insTCTT 3_prime_UTR_variant 9/9 ENST00000610140.7 NP_001002010.2 Q9H0P0

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NT5C3AENST00000610140.7 linkuse as main transcriptc.*224_*225insTCTT 3_prime_UTR_variant 9/91 NM_001002010.5 ENSP00000476480.2 X6RM59

Frequencies

GnomAD3 genomes
AF:
0.754
AC:
108944
AN:
144406
Hom.:
39553
Cov.:
0
show subpopulations
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
GnomAD3 exomes
AF:
0.612
AC:
51064
AN:
83480
Hom.:
14778
AF XY:
0.602
AC XY:
26980
AN XY:
44784
show subpopulations
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 SAS exome
AF:
0.525
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
show subpopulations
Gnomad4 AFR exome
AF:
0.731
Gnomad4 AMR exome
AF:
0.735
Gnomad4 ASJ exome
AF:
0.553
Gnomad4 EAS exome
AF:
0.640
Gnomad4 SAS exome
AF:
0.652
Gnomad4 FIN exome
AF:
0.708
Gnomad4 NFE exome
AF:
0.663
Gnomad4 OTH exome
AF:
0.656
GnomAD4 genome
AF:
0.755
AC:
109043
AN:
144518
Hom.:
39596
Cov.:
0
AF XY:
0.756
AC XY:
53338
AN XY:
70546
show subpopulations
Gnomad4 AFR
AF:
0.811
Gnomad4 AMR
AF:
0.769
Gnomad4 ASJ
AF:
0.599
Gnomad4 EAS
AF:
0.691
Gnomad4 SAS
AF:
0.709
Gnomad4 FIN
AF:
0.776
Gnomad4 NFE
AF:
0.732
Gnomad4 OTH
AF:
0.729
Bravo
AF:
0.725

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 19, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

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