rs373800800
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001142.2(AMELX):c.280G>A(p.Val94Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,208,188 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001142.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMELX | NM_001142.2 | c.280G>A | p.Val94Met | missense_variant | 5/6 | ENST00000380714.7 | |
ARHGAP6 | NM_013427.3 | c.589-43976C>T | intron_variant | ENST00000337414.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMELX | ENST00000380714.7 | c.280G>A | p.Val94Met | missense_variant | 5/6 | 1 | NM_001142.2 | P1 | |
ARHGAP6 | ENST00000337414.9 | c.589-43976C>T | intron_variant | 1 | NM_013427.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000637 AC: 7AN: 109931Hom.: 0 Cov.: 21 AF XY: 0.0000621 AC XY: 2AN XY: 32207
GnomAD3 exomes AF: 0.0000272 AC: 5AN: 183514Hom.: 0 AF XY: 0.0000294 AC XY: 2AN XY: 67940
GnomAD4 exome AF: 0.0000373 AC: 41AN: 1098257Hom.: 0 Cov.: 33 AF XY: 0.0000303 AC XY: 11AN XY: 363611
GnomAD4 genome ? AF: 0.0000637 AC: 7AN: 109931Hom.: 0 Cov.: 21 AF XY: 0.0000621 AC XY: 2AN XY: 32207
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at