dbSNP rs7639267: NT5DC2:n.-136C>A (chr3-52534789-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_022908.3(NT5DC2):c.-136C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 1,111,396 control chromosomes in the GnomAD database, including 172,965 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 ( 26515 hom., cov: 33)

Exomes 𝑓: 0.55 ( 146450 hom. )

Consequence

NT5DC2
NM_022908.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0160

Publications

22 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:

UQCC5 (HGNC:37257): (ubiquinol-cytochrome c reductase complex assembly factor 5) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

UQCC5 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022908.3. 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_022908.3		c.-136C>A		5_prime_UTR	Exon 1 of 14	NP_075059.1	Q9H857-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NT5DC2	ENST00000492555.5	TSL:1	n.-136C>A	non_coding_transcript_exon	Exon 1 of 13	ENSP00000419774.1	F8WEY1
NT5DC2	ENST00000492555.5	TSL:1	n.-136C>A	5_prime_UTR	Exon 1 of 13	ENSP00000419774.1	F8WEY1
NT5DC2	ENST00000307076.8	TSL:2	c.-136C>A	5_prime_UTR	Exon 1 of 14	ENSP00000302468.4	Q9H857-1

Frequencies

GnomAD3 genomes

AF:

0.586

AC:

88968

AN:

151944

Hom.:

26477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.657

Gnomad AMI

AF:

0.575

Gnomad AMR

AF:

0.643

Gnomad ASJ

AF:

0.552

Gnomad EAS

AF:

0.452

Gnomad SAS

AF:

0.333

Gnomad FIN

AF:

0.545

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.565

Gnomad OTH

AF:

0.579

GnomAD4 exome

AF:

0.547

AC:

524569

AN:

959334

Hom.:

146450

Cov.:

AF XY:

0.539

AC XY:

261009

AN XY:

484374

show subpopulations

African (AFR)

AF:

0.668

AC:

15168

AN:

22722

American (AMR)

AF:

0.650

AC:

18824

AN:

28946

Ashkenazi Jewish (ASJ)

AF:

0.551

AC:

9721

AN:

17628

East Asian (EAS)

AF:

0.493

AC:

18164

AN:

36872

South Asian (SAS)

AF:

0.339

AC:

21271

AN:

62706

European-Finnish (FIN)

AF:

0.554

AC:

19207

AN:

34696

Middle Eastern (MID)

AF:

0.532

AC:

2097

AN:

3944

European-Non Finnish (NFE)

AF:

0.560

AC:

396833

AN:

708696

Other (OTH)

AF:

0.540

AC:

23284

AN:

43124

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

11721

23442

35163

46884

58605

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9626

19252

28878

38504

48130

<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:

0.586

AC:

89065

AN:

152062

Hom.:

26515

Cov.:

AF XY:

0.581

AC XY:

43187

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.658

AC:

27270

AN:

41468

American (AMR)

AF:

0.643

AC:

9828

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.552

AC:

1913

AN:

3468

East Asian (EAS)

AF:

0.452

AC:

2338

AN:

5168

South Asian (SAS)

AF:

0.333

AC:

1608

AN:

4824

European-Finnish (FIN)

AF:

0.545

AC:

5751

AN:

10560

Middle Eastern (MID)

AF:

0.599

AC:

176

AN:

294

European-Non Finnish (NFE)

AF:

0.565

AC:

38427

AN:

67972

Other (OTH)

AF:

0.583

AC:

1230

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1927

3854

5780

7707

9634

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

738

1476

2214

2952

3690

<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:

0.584

Hom.:

13880

Bravo

AF:

0.600

Asia WGS

AF:

0.456

AC:

1590

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

4.6

(source)

DANN

Benign

0.63

PhyloP100

-0.016

PromoterAI

0.013

Neutral

(source)

Mutation Taster

=300/0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over