chrX-64189929-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_152424.4(AMER1):āc.3358C>Gā(p.Leu1120Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000831 in 1,203,999 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_152424.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AMER1 | NM_152424.4 | c.3358C>G | p.Leu1120Val | missense_variant | 2/2 | ENST00000374869.8 | NP_689637.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AMER1 | ENST00000374869.8 | c.3358C>G | p.Leu1120Val | missense_variant | 2/2 | 5 | NM_152424.4 | ENSP00000364003.4 |
Frequencies
GnomAD3 genomes AF: 0.00000911 AC: 1AN: 109776Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32020
GnomAD4 exome AF: 0.00000823 AC: 9AN: 1094223Hom.: 0 Cov.: 35 AF XY: 0.00000833 AC XY: 3AN XY: 360127
GnomAD4 genome AF: 0.00000911 AC: 1AN: 109776Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32020
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 24, 2024 | The c.3358C>G (p.L1120V) alteration is located in exon 2 (coding exon 1) of the AMER1 gene. This alteration results from a C to G substitution at nucleotide position 3358, causing the leucine (L) at amino acid position 1120 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at