13-25170144-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152704.4(AMER2):c.1476G>T(p.Arg492Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,772 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMER2 | NM_152704.4 | c.1476G>T | p.Arg492Ser | missense_variant | 1/1 | ENST00000515384.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMER2 | ENST00000515384.2 | c.1476G>T | p.Arg492Ser | missense_variant | 1/1 | NM_152704.4 | P1 | ||
LINC01053 | ENST00000656176.1 | n.63+1113C>A | intron_variant, non_coding_transcript_variant | ||||||
AMER2 | ENST00000357816.2 | c.1119G>T | p.Arg373Ser | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251090Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135746
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461772Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727192
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 29, 2024 | The c.1476G>T (p.R492S) alteration is located in exon 1 (coding exon 1) of the AMER2 gene. This alteration results from a G to T substitution at nucleotide position 1476, causing the arginine (R) at amino acid position 492 to be replaced by a serine (S). 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