rs4282054

Variant names:

• chr3-52532049-T-A
• NM_001134231.2:c.232+1457A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-52532049-T-A
• chr3-52532049-T-C
• chr3-52532049-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001134231.2(NT5DC2):​c.232+1457A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NT5DC2	NM_001134231.2	c.232+1457A>T		intron_variant	Intron 1 of 13	ENST00000422318.7	NP_001127703.1
NT5DC2	NM_022908.3	c.121+2484A>T		intron_variant	Intron 1 of 13		NP_075059.1
NT5DC2	XM_006713303.4	c.232+1457A>T		intron_variant	Intron 1 of 13		XP_006713366.1
NT5DC2	XM_047448760.1	c.121+2484A>T		intron_variant	Intron 1 of 13		XP_047304716.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5DC2	ENST00000422318.7	c.232+1457A>T		intron_variant	Intron 1 of 13	5	NM_001134231.2	ENSP00000406933.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 154448 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 74132

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.56

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-52566065;