chr17-42954888-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001261434.2(AARSD1):c.941T>C(p.Val314Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000135 in 1,614,032 control chromosomes in the GnomAD database, including 1 homozygotes. 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_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.941T>C | p.Val314Ala | missense_variant | 9/12 | ENST00000427569.7 | |
PTGES3L-AARSD1 | NM_001136042.2 | c.1463T>C | p.Val488Ala | missense_variant | 14/17 | ||
PTGES3L-AARSD1 | NM_025267.4 | c.1280T>C | p.Val427Ala | missense_variant | 14/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AARSD1 | ENST00000427569.7 | c.941T>C | p.Val314Ala | missense_variant | 9/12 | 5 | NM_001261434.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000239 AC: 60AN: 251464Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135900
GnomAD4 exome AF: 0.000132 AC: 193AN: 1461798Hom.: 1 Cov.: 31 AF XY: 0.000139 AC XY: 101AN XY: 727188
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74430
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.1463T>C (p.V488A) alteration is located in exon 14 (coding exon 14) of the AARSD1 gene. This alteration results from a T to C substitution at nucleotide position 1463, causing the valine (V) at amino acid position 488 to be replaced by an alanine (A). 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