rs549332

chr6-116133425-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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]

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
NT5DC1	NM_152729.3	c.529+15480G>A		intron_variant		ENST00000319550.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5DC1	ENST00000319550.9	c.529+15480G>A		intron_variant		1	NM_152729.3	P1
COL10A1	ENST00000418500.1	c.-15-7918C>T		intron_variant		3
NT5DC1	ENST00000419791.3	c.530-12013G>A		intron_variant		3
NT5DC1	ENST00000460749.1	c.27+15480G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100568 AN: 151838 Hom.: 35488 Cov.: 31

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.: 31 AF XY: 0.655 AC XY: 48638 AN XY: 74270

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.633

Alfa AF: 0.596 Hom.: 37980

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
Dann	Benign	0.56

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

LitVar

Other links and lift over

dbSNP: rs549332; hg19: chr6-116454588;