rs1272345829
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_198488.5(FAM83H):c.3403C>T(p.Arg1135Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000496 in 1,612,246 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198488.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM83H | ENST00000388913.4 | c.3403C>T | p.Arg1135Cys | missense_variant | Exon 5 of 5 | 5 | NM_198488.5 | ENSP00000373565.3 | ||
FAM83H | ENST00000650760.1 | c.4006C>T | p.Arg1336Cys | missense_variant | Exon 5 of 5 | ENSP00000499217.1 | ||||
FAM83H | ENST00000395103.2 | n.2581C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 | ENSP00000378535.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000819 AC: 2AN: 244314Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133648
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460046Hom.: 0 Cov.: 83 AF XY: 0.00000551 AC XY: 4AN XY: 726318
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: FAM83H c.3403C>T (p.Arg1135Cys) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8.2e-06 in 244314 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.3403C>T in individuals affected with Amelogenesis Imperfecta, Hypocalcification Type and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at