chr6-116119047-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000493.4(COL10A1):c.*1026G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0513 in 152,610 control chromosomes in the GnomAD database, including 230 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.051 ( 230 hom., cov: 33)
Exomes 𝑓: 0.026 ( 0 hom. )
Consequence
COL10A1
NM_000493.4 3_prime_UTR
NM_000493.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0250
Genes affected
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 6-116119047-C-T is Benign according to our data. Variant chr6-116119047-C-T is described in ClinVar as [Benign]. Clinvar id is 355069.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0592 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL10A1 | NM_000493.4 | c.*1026G>A | 3_prime_UTR_variant | 3/3 | ENST00000651968.1 | ||
NT5DC1 | NM_152729.3 | c.529+1102C>T | intron_variant | ENST00000319550.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL10A1 | ENST00000651968.1 | c.*1026G>A | 3_prime_UTR_variant | 3/3 | NM_000493.4 | P1 | |||
NT5DC1 | ENST00000319550.9 | c.529+1102C>T | intron_variant | 1 | NM_152729.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0513 AC: 7803AN: 152070Hom.: 229 Cov.: 33
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GnomAD4 exome AF: 0.0261 AC: 11AN: 422Hom.: 0 Cov.: 0 AF XY: 0.0354 AC XY: 9AN XY: 254
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GnomAD4 genome AF: 0.0513 AC: 7812AN: 152188Hom.: 230 Cov.: 33 AF XY: 0.0503 AC XY: 3744AN XY: 74404
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Metaphyseal chondrodysplasia, Schmid type Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at