dbSNP rs549332: NT5DC1:c.529+15480G>A (chr6-116133425-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_152729.3(NT5DC1):c.529+15480G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 151,958 control chromosomes in the GnomAD database, including 35,542 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 0.66 ( 35542 hom., cov: 31)

Consequence

NT5DC1
NM_152729.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14

Publications

12 publications found

Variant links:

Genes affected

NT5DC1 (HGNC:21556): (5'-nucleotidase domain containing 1) While the exact function of the protein encoded by this gene is not known, it belongs to the 5'(3')-deoxyribonucleotidase family. [provided by RefSeq, May 2010]

NT5DC1 links:

COL10A1 (HGNC:2185): (collagen type X alpha 1 chain) This gene encodes the alpha chain of type X collagen, a short chain collagen expressed by hypertrophic chondrocytes during endochondral ossification. Unlike type VIII collagen, the other short chain collagen, type X collagen is a homotrimer. Mutations in this gene are associated with Schmid type metaphyseal chondrodysplasia (SMCD) and Japanese type spondylometaphyseal dysplasia (SMD). [provided by RefSeq, Jul 2008]

COL10A1 Gene-Disease associations (from GenCC):

Schmid metaphyseal chondrodysplasia
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Orphanet, Labcorp Genetics (formerly Invitae)

COL10A1 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NT5DC1	NM_152729.3 link	c.529+15480G>A		intron_variant	Intron 6 of 11	ENST00000319550.9	NP_689942.2	Q5TFE4-1Q9H2R1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
NT5DC1	ENST00000319550.9 link	c.529+15480G>A	intron_variant	Intron 6 of 11	1	NM_152729.3	ENSP00000326858.3	Q5TFE4-1
NT5DC1	ENST00000419791.3 link	c.530-12013G>A	intron_variant	Intron 6 of 6	3		ENSP00000393578.1	Q5QPD0
COL10A1	ENST00000418500.1 link	c.-15-7918C>T	intron_variant	Intron 1 of 1	3		ENSP00000392712.1	Q5QPC8
NT5DC1	ENST00000460749.1 link	n.25+15480G>A	intron_variant	Intron 1 of 6	5		ENSP00000433238.1	H0YDA5

Frequencies

GnomAD3 genomes

AF:

0.662

AC:

100568

AN:

151838

Hom.:

35488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.922

Gnomad AMI

AF:

0.441

Gnomad AMR

AF:

0.581

Gnomad ASJ

AF:

0.686

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.514

Gnomad FIN

AF:

0.534

Gnomad MID

AF:

0.631

Gnomad NFE

AF:

0.580

Gnomad OTH

AF:

0.634

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.662

AC:

100670

AN:

151958

Hom.:

35542

Cov.:

AF XY:

0.655

AC XY:

48638

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.923

AC:

38311

AN:

41524

American (AMR)

AF:

0.580

AC:

8852

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.686

AC:

2381

AN:

3470

East Asian (EAS)

AF:

0.332

AC:

1714

AN:

5164

South Asian (SAS)

AF:

0.513

AC:

2453

AN:

4780

European-Finnish (FIN)

AF:

0.534

AC:

5633

AN:

10552

Middle Eastern (MID)

AF:

0.623

AC:

182

AN:

292

European-Non Finnish (NFE)

AF:

0.580

AC:

39416

AN:

67918

Other (OTH)

AF:

0.633

AC:

1330

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1556

3112

4667

6223

7779

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

776

1552

2328

3104

3880

<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:

0.606

Hom.:

49753

Bravo

AF:

0.677

Asia WGS

AF:

0.521

AC:

1809

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.11

(source)

DANN

Benign

0.56

PhyloP100

-1.1

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over