rs4282054

Variant names:

• chr3-52532049-T-A
• rs4282054
• 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. The variant received -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
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134231.2. 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
	NT5DC2	NM_001134231.2	MANE Select	c.232+1457A>T		intron	N/A	NP_001127703.1	Q9H857-2
	NT5DC2	NM_022908.3		c.121+2484A>T		intron	N/A	NP_075059.1	Q9H857-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NT5DC2	ENST00000422318.7	TSL:5 MANE Select	c.232+1457A>T		intron	N/A	ENSP00000406933.2	Q9H857-2
	NT5DC2	ENST00000459839.5	TSL:1	c.232+1457A>T		intron	N/A	ENSP00000419547.1	Q9H857-3
	NT5DC2	ENST00000492555.5	TSL:1	n.303+2302A>T		intron	N/A	ENSP00000419774.1	F8WEY1

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

African (AFR) AF: 0.00 AC: 0 AN: 2760

American (AMR) AF: 0.00 AC: 0 AN: 162

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 998

East Asian (EAS) AF: 0.00 AC: 0 AN: 644

South Asian (SAS) AF: 0.00 AC: 0 AN: 3004

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 58

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 304

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 141514

Other (OTH) AF: 0.00 AC: 0 AN: 5004

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.56
PhyloP100		-5.7

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

Other links and lift over

dbSNP: rs4282054; hg19: chr3-52566065;