chr13-25170488-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_152704.4(AMER2):āc.1132C>Gā(p.Leu378Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,614,078 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 Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L378I) has been classified as Uncertain significance.
Frequency
Consequence
NM_152704.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMER2 | NM_152704.4 | c.1132C>G | p.Leu378Val | missense_variant | 1/1 | ENST00000515384.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMER2 | ENST00000515384.2 | c.1132C>G | p.Leu378Val | missense_variant | 1/1 | NM_152704.4 | P1 | ||
LINC01053 | ENST00000656176.1 | n.63+1457G>C | intron_variant, non_coding_transcript_variant | ||||||
AMER2 | ENST00000357816.2 | c.782-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250326Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135760
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 727248
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | The c.1132C>G (p.L378V) alteration is located in exon 1 (coding exon 1) of the AMER2 gene. This alteration results from a C to G substitution at nucleotide position 1132, causing the leucine (L) at amino acid position 378 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