17-41830878-T-C

Position:

• chr17-41830878-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_052935.5(NT5C3B):​c.327A>G​(p.Ala109Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.908 in 1,602,722 control chromosomes in the GnomAD database, including 661,584 homozygotes. 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: 𝑓 0.90 (61278 hom., cov: 31)
  • Exomes 𝑓: 0.91 (600306 hom.)
• Consequence: NT5C3B NM_052935.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.63

Genes affected

NT5C3B (HGNC:28300): (5'-nucleotidase, cytosolic IIIB) Predicted to enable 5'-nucleotidase activity. Predicted to be involved in exonucleolytic catabolism of deadenylated mRNA. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

NT5C3B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP7: Synonymous conserved (PhyloP=-3.63 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5C3B	NM_052935.5	c.327A>G	p.Ala109Ala	synonymous_variant	6/9	ENST00000435506.7	NP_443167.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C3B	ENST00000435506.7	c.327A>G	p.Ala109Ala	synonymous_variant	6/9	5	NM_052935.5	ENSP00000389948.2

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136285 AN: 152050 Hom.: 61228 Cov.: 31

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.896

GnomAD3 exomes AF: 0.918 AC: 226652 AN: 246970 Hom.: 104201 AF XY: 0.918 AC XY: 122863 AN XY: 133826

Gnomad AFR exome AF: 0.851

Gnomad AMR exome AF: 0.942

Gnomad ASJ exome AF: 0.926

Gnomad EAS exome AF: 1.00

Gnomad SAS exome AF: 0.944

Gnomad FIN exome AF: 0.878

Gnomad NFE exome AF: 0.907

Gnomad OTH exome AF: 0.914

GnomAD4 exome AF: 0.909 AC: 1319092 AN: 1450554 Hom.: 600306 Cov.: 31 AF XY: 0.910 AC XY: 657525 AN XY: 722360

Gnomad4 AFR exome AF: 0.847

Gnomad4 AMR exome AF: 0.940

Gnomad4 ASJ exome AF: 0.925

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.942

Gnomad4 FIN exome AF: 0.883

Gnomad4 NFE exome AF: 0.905

Gnomad4 OTH exome AF: 0.909

GnomAD4 genome AF: 0.896 AC: 136392 AN: 152168 Hom.: 61278 Cov.: 31 AF XY: 0.897 AC XY: 66712 AN XY: 74404

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.949

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.898

Alfa AF: 0.904 Hom.: 74836

Bravo AF: 0.898

Asia WGS AF: 0.973 AC: 3385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.23
DANN	Benign	0.57
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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

Publications

LitVar

Other links and lift over

dbSNP: rs4796712; hg19: chr17-39987130;