Genetic Variant NT5DC2:c.232+1457A>G (chr3-52532049-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	MANE	Protein	UniProt
NT5DC2	NM_001134231.2 link	c.232+1457A>G	intron_variant	Intron 1 of 13	ENST00000422318.7	NP_001127703.1	Q9H857-2
NT5DC2	NM_022908.3 link	c.121+2484A>G	intron_variant	Intron 1 of 13		NP_075059.1	Q9H857-1
NT5DC2	XM_006713303.4 link	c.232+1457A>G	intron_variant	Intron 1 of 13		XP_006713366.1
NT5DC2	XM_047448760.1 link	c.121+2484A>G	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>G		intron_variant	Intron 1 of 13	5	NM_001134231.2	ENSP00000406933.2		Q9H857-2

Frequencies

GnomAD3 genomes

AF:

0.585

AC:

88802

AN:

151760

Hom.:

26380

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.685

AC:

1884

AN:

2752

American (AMR)

AF:

0.611

AC:

AN:

162

Ashkenazi Jewish (ASJ)

AF:

0.565

AC:

562

AN:

994

East Asian (EAS)

AF:

0.467

AC:

300

AN:

642

South Asian (SAS)

AF:

0.361

AC:

1079

AN:

2992

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.549

AC:

167

AN:

304

European-Non Finnish (NFE)

AF:

0.558

AC:

78603

AN:

140818

Other (OTH)

AF:

0.545

AC:

2719

AN:

4988

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1864

3728

5591

7455

9319

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2994

5988

8982

11976

14970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.585

AC:

88898

AN:

151878

Hom.:

26418

Cov.:

AF XY:

0.581

AC XY:

43106

AN XY:

74222

show subpopulations

African (AFR)

AF:

0.659

AC:

27250

AN:

41378

American (AMR)

AF:

0.638

AC:

9739

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.552

AC:

1913

AN:

3468

East Asian (EAS)

AF:

0.454

AC:

2338

AN:

5152

South Asian (SAS)

AF:

0.343

AC:

1648

AN:

4798

European-Finnish (FIN)

AF:

0.545

AC:

5746

AN:

10548

Middle Eastern (MID)

AF:

0.599

AC:

176

AN:

294

European-Non Finnish (NFE)

AF:

0.564

AC:

38342

AN:

67950

Other (OTH)

AF:

0.581

AC:

1225

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1924

3848

5772

7696

9620

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

736

1472

2208

2944

3680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.605

Hom.:

6705

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

(source)

DANN

Benign

0.41

PhyloP100

-5.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over