19-2249331-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000479.5(AMH):c.-2C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 1,561,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_000479.5 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AMH | ENST00000221496 | c.-2C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 5 | 1 | NM_000479.5 | ENSP00000221496.2 | |||
AMH | ENST00000221496 | c.-2C>T | 5_prime_UTR_variant | Exon 1 of 5 | 1 | NM_000479.5 | ENSP00000221496.2 | |||
AMH | ENST00000592877.1 | n.23C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000214 AC: 36AN: 168098Hom.: 0 AF XY: 0.000175 AC XY: 16AN XY: 91574
GnomAD4 exome AF: 0.000305 AC: 429AN: 1408842Hom.: 0 Cov.: 30 AF XY: 0.000284 AC XY: 198AN XY: 697012
GnomAD4 genome AF: 0.000158 AC: 24AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74354
ClinVar
Submissions by phenotype
AMH-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at