19-2249385-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000479.5(AMH):c.53C>T(p.Ala18Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,588,802 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A18T) has been classified as Uncertain significance.
Frequency
Consequence
NM_000479.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00105 AC: 159AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00101 AC: 208AN: 206108Hom.: 0 AF XY: 0.00101 AC XY: 113AN XY: 112066
GnomAD4 exome AF: 0.00144 AC: 2069AN: 1436546Hom.: 2 Cov.: 30 AF XY: 0.00139 AC XY: 992AN XY: 712534
GnomAD4 genome AF: 0.00104 AC: 158AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.00102 AC XY: 76AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at