chr5-168506153-T-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002887.4(RARS1):c.1190T>A(p.Phe397Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,579,038 control chromosomes in the GnomAD database, including 23,808 homozygotes. 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 Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_002887.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RARS1 | ENST00000231572.8 | c.1190T>A | p.Phe397Tyr | missense_variant | Exon 10 of 15 | 1 | NM_002887.4 | ENSP00000231572.3 | ||
RARS1 | ENST00000520013.5 | n.*691T>A | non_coding_transcript_exon_variant | Exon 9 of 14 | 2 | ENSP00000429030.1 | ||||
RARS1 | ENST00000520013.5 | n.*691T>A | 3_prime_UTR_variant | Exon 9 of 14 | 2 | ENSP00000429030.1 |
Frequencies
GnomAD3 genomes AF: 0.130 AC: 19782AN: 152014Hom.: 1711 Cov.: 32
GnomAD3 exomes AF: 0.138 AC: 31307AN: 227456Hom.: 2718 AF XY: 0.140 AC XY: 17178AN XY: 123040
GnomAD4 exome AF: 0.168 AC: 240294AN: 1426906Hom.: 22096 Cov.: 31 AF XY: 0.166 AC XY: 117867AN XY: 709822
GnomAD4 genome AF: 0.130 AC: 19782AN: 152132Hom.: 1712 Cov.: 32 AF XY: 0.127 AC XY: 9436AN XY: 74376
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 24, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 03, 2025 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at