rs17000647
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_178497.5(ODAPH):c.67+371C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0218 in 1,530,292 control chromosomes in the GnomAD database, including 446 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 0.016 ( 25 hom., cov: 32)
Exomes 𝑓: 0.022 ( 421 hom. )
Consequence
ODAPH
NM_178497.5 intron
NM_178497.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.110
Genes affected
ODAPH (HGNC:26300): (odontogenesis associated phosphoprotein) Dental enamel forms the outer cap of teeth and is the hardest substance found in vertebrates. This gene is thought to encode an extracellular matrix acidic phosphoprotein that has a function in enamel mineralization during amelogenesis. Mutations in this gene are associated with recessive hypomineralized amelogenesis imperfecta. [provided by RefSeq, Oct 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0164 (2501/152318) while in subpopulation NFE AF= 0.0259 (1759/68036). AF 95% confidence interval is 0.0248. There are 25 homozygotes in gnomad4. There are 1153 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 25 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ODAPH | NM_178497.5 | c.67+371C>A | intron_variant | ENST00000311623.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ODAPH | ENST00000311623.9 | c.67+371C>A | intron_variant | 1 | NM_178497.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0164 AC: 2501AN: 152200Hom.: 25 Cov.: 32
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GnomAD3 exomes AF: 0.0152 AC: 1955AN: 128544Hom.: 28 AF XY: 0.0148 AC XY: 1040AN XY: 70386
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GnomAD4 exome AF: 0.0224 AC: 30826AN: 1377974Hom.: 421 Cov.: 29 AF XY: 0.0220 AC XY: 14968AN XY: 680296
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GnomAD4 genome ? AF: 0.0164 AC: 2501AN: 152318Hom.: 25 Cov.: 32 AF XY: 0.0155 AC XY: 1153AN XY: 74480
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ClinVar
Not reported inComputational scores
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Name
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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