chr13-25170276-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_152704.4(AMER2):c.1344G>T(p.Glu448Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,613,330 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_152704.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMER2 | NM_152704.4 | c.1344G>T | p.Glu448Asp | missense_variant | 1/1 | ENST00000515384.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMER2 | ENST00000515384.2 | c.1344G>T | p.Glu448Asp | missense_variant | 1/1 | NM_152704.4 | P1 | ||
LINC01053 | ENST00000656176.1 | n.63+1245C>A | intron_variant, non_coding_transcript_variant | ||||||
AMER2 | ENST00000357816.2 | c.987G>T | p.Glu329Asp | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249002Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134832
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461214Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726850
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74292
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at