rs13254035
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_198488.5(FAM83H):c.1827C>T(p.Tyr609=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 1,580,832 control chromosomes in the GnomAD database, including 722,428 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.83 ( 56385 hom., cov: 33)
Exomes 𝑓: 0.96 ( 666043 hom. )
Consequence
FAM83H
NM_198488.5 synonymous
NM_198488.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.315
Genes affected
FAM83H (HGNC:24797): (family with sequence similarity 83 member H) The protein encoded by this gene plays an important role in the structural development and calcification of tooth enamel. Defects in this gene are a cause of amelogenesis imperfecta type 3 (AI3). [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 8-143727634-G-A is Benign according to our data. Variant chr8-143727634-G-A is described in ClinVar as [Benign]. Clinvar id is 263133.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-143727634-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.315 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM83H | NM_198488.5 | c.1827C>T | p.Tyr609= | synonymous_variant | 5/5 | ENST00000388913.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM83H | ENST00000388913.4 | c.1827C>T | p.Tyr609= | synonymous_variant | 5/5 | 5 | NM_198488.5 | P2 | |
FAM83H | ENST00000650760.1 | c.2430C>T | p.Tyr810= | synonymous_variant | 5/5 | A2 | |||
FAM83H | ENST00000395103.2 | c.1008C>T | p.Tyr336= | synonymous_variant, NMD_transcript_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.832 AC: 126390AN: 151942Hom.: 56383 Cov.: 33
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GnomAD3 exomes AF: 0.945 AC: 184387AN: 195098Hom.: 88402 AF XY: 0.950 AC XY: 103631AN XY: 109084
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GnomAD4 exome AF: 0.962 AC: 1374726AN: 1428782Hom.: 666043 Cov.: 70 AF XY: 0.963 AC XY: 683560AN XY: 709768
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GnomAD4 genome ? AF: 0.831 AC: 126415AN: 152050Hom.: 56385 Cov.: 33 AF XY: 0.837 AC XY: 62225AN XY: 74322
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Amelogenesis imperfecta, hypocalcification type Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Jul 28, 2017 | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Computational scores
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BayesDel_noAF
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