Genetic Variant NT5DC2:c.232+1457A>C (chr3-52532049-T-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001134231.2(NT5DC2):c.232+1457A>C 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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.73

Publications

25 publications found

Variant links:

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]

NT5DC2 links:

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ACMG classification

Classification was made for transcript

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=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
NT5DC2	NM_001134231.2 link	c.232+1457A>C	intron_variant	Intron 1 of 13	ENST00000422318.7	NP_001127703.1	Q9H857-2
NT5DC2	NM_022908.3 link	c.121+2484A>C	intron_variant	Intron 1 of 13		NP_075059.1	Q9H857-1
NT5DC2	XM_006713303.4 link	c.232+1457A>C	intron_variant	Intron 1 of 13		XP_006713366.1
NT5DC2	XM_047448760.1 link	c.121+2484A>C	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 link	c.232+1457A>C		intron_variant	Intron 1 of 13	5	NM_001134231.2	ENSP00000406933.2		Q9H857-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

154448

Hom.:

AF XY:

0.00

AC XY:

AN XY:

74132

African (AFR)

AF:

0.00

AC:

AN:

2760

American (AMR)

AF:

0.00

AC:

AN:

162

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

998

East Asian (EAS)

AF:

0.00

AC:

AN:

644

South Asian (SAS)

AF:

0.00

AC:

AN:

3004

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

304

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

141514

Other (OTH)

AF:

0.00

AC:

AN:

5004

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

6705

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.28

(source)

DANN

Benign

0.50

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over