rs4282054

chr3-52532049-T-Cchr3-52532049-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001134231.2(NT5DC2):c.232+1457A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 305,586 control chromosomes in the GnomAD database, including 50,488 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 0.59 (26418 hom., cov: 31)
  • Exomes 𝑓: 0.56 (24070 hom.)
• Consequence: NT5DC2 NM_001134231.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.73

Genes affected

NT5DC2 (HGNC:25717): (5'-nucleotidase domain containing 2) Predicted to enable 5'-nucleotidase activity. Predicted to be involved in dephosphorylation. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5DC2	NM_001134231.2	c.232+1457A>G		intron_variant		ENST00000422318.7
NT5DC2	NM_022908.3	c.121+2484A>G		intron_variant
NT5DC2	XM_006713303.4	c.232+1457A>G		intron_variant
NT5DC2	XM_047448760.1	c.121+2484A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5DC2	ENST00000422318.7	c.232+1457A>G		intron_variant		5	NM_001134231.2	P2

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88802 AN: 151760 Hom.: 26380 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.576

GnomAD4 exome AF: 0.556 AC: 85441 AN: 153708 Hom.: 24070 AF XY: 0.557 AC XY: 41064 AN XY: 73772

Gnomad4 AFR exome AF: 0.685

Gnomad4 AMR exome AF: 0.611

Gnomad4 ASJ exome AF: 0.565

Gnomad4 EAS exome AF: 0.467

Gnomad4 SAS exome AF: 0.361

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.558

Gnomad4 OTH exome AF: 0.545

GnomAD4 genome AF: 0.585 AC: 88898 AN: 151878 Hom.: 26418 Cov.: 31 AF XY: 0.581 AC XY: 43106 AN XY: 74222

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.581

Alfa AF: 0.575 Hom.: 3728

Bravo AF: 0.599

Asia WGS AF: 0.463 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.32
Dann	Benign	0.41

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: rs4282054; hg19: chr3-52566065;