rs12204816

Variant names:

• chr6-116140475-C-T
• rs12204816
• NM_152729.3:c.529+22530C>T

Variant summary

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

The NM_152729.3(NT5DC1):​c.529+22530C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,012 control chromosomes in the GnomAD database, including 2,182 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 0.14 (2182 hom., cov: 32)
• Consequence: NT5DC1 NM_152729.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NT5DC1	NM_152729.3	c.529+22530C>T		intron_variant	Intron 6 of 11	ENST00000319550.9	NP_689942.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5DC1	ENST00000319550.9	c.529+22530C>T		intron_variant	Intron 6 of 11	1	NM_152729.3	ENSP00000326858.3
NT5DC1	ENST00000419791.3	c.530-4963C>T		intron_variant	Intron 6 of 6	3		ENSP00000393578.1
COL10A1	ENST00000418500.1	c.-15-14968G>A		intron_variant	Intron 1 of 1	3		ENSP00000392712.1
NT5DC1	ENST00000460749.1	n.25+22530C>T		intron_variant	Intron 1 of 6	5		ENSP00000433238.1

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21804 AN: 151894 Hom.: 2182 Cov.: 32

Gnomad AFR AF: 0.0429

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0387

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.143 AC: 21801 AN: 152012 Hom.: 2182 Cov.: 32 AF XY: 0.136 AC XY: 10106 AN XY: 74312

Gnomad4 AFR AF: 0.0428

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0392

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.173

Alfa AF: 0.198 Hom.: 1867

Bravo AF: 0.147

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.16
DANN	Benign	0.16

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: rs12204816; hg19: chr6-116461638; COSMIC: COSV60311888; COSMIC: COSV60311888;