chr6-116126193-C-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_152729.3(NT5DC1):c.529+8248C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,106 control chromosomes in the GnomAD database, including 5,754 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 0.26 ( 5752 hom., cov: 32)
Exomes 𝑓: 0.20 ( 2 hom. )
Consequence
NT5DC1
NM_152729.3 intron
NM_152729.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.16
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NT5DC1 | NM_152729.3 | c.529+8248C>G | intron_variant | ENST00000319550.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NT5DC1 | ENST00000319550.9 | c.529+8248C>G | intron_variant | 1 | NM_152729.3 | P1 | |||
COL10A1 | ENST00000418500.1 | c.-15-686G>C | intron_variant | 3 | |||||
NT5DC1 | ENST00000419791.3 | c.529+8248C>G | intron_variant | 3 | |||||
NT5DC1 | ENST00000460749.1 | c.27+8248C>G | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.264 AC: 40103AN: 151934Hom.: 5746 Cov.: 32
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GnomAD4 exome AF: 0.204 AC: 11AN: 54Hom.: 2 AF XY: 0.229 AC XY: 11AN XY: 48
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GnomAD4 genome AF: 0.264 AC: 40138AN: 152052Hom.: 5752 Cov.: 32 AF XY: 0.256 AC XY: 19014AN XY: 74354
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at