chr17-42950649-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001261434.2(AARSD1):c.1183A>C(p.Met395Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001261434.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AARSD1 | NM_001261434.2 | c.1183A>C | p.Met395Leu | missense_variant | 12/12 | ENST00000427569.7 | |
PTGES3L-AARSD1 | NM_001136042.2 | c.1705A>C | p.Met569Leu | missense_variant | 17/17 | ||
PTGES3L-AARSD1 | NM_025267.4 | c.1522A>C | p.Met508Leu | missense_variant | 17/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AARSD1 | ENST00000427569.7 | c.1183A>C | p.Met395Leu | missense_variant | 12/12 | 5 | NM_001261434.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251292Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135824
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461826Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727218
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 09, 2023 | The c.1705A>C (p.M569L) alteration is located in exon 17 (coding exon 17) of the AARSD1 gene. This alteration results from a A to C substitution at nucleotide position 1705, causing the methionine (M) at amino acid position 569 to be replaced by a leucine (L). 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