7-30595016-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The ENST00000389266.8(GARS1):āc.95T>Cā(p.Leu32Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000701 in 1,426,720 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 Benign (no stars).
Frequency
Consequence
ENST00000389266.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GARS1 | NM_002047.4 | c.95T>C | p.Leu32Pro | missense_variant | 1/17 | ENST00000389266.8 | NP_002038.2 | |
GARS1 | NM_001316772.1 | c.-68T>C | 5_prime_UTR_variant | 1/17 | NP_001303701.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GARS1 | ENST00000389266.8 | c.95T>C | p.Leu32Pro | missense_variant | 1/17 | 1 | NM_002047.4 | ENSP00000373918 | P2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000520 AC: 1AN: 192172Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 106338
GnomAD4 exome AF: 0.00000701 AC: 10AN: 1426720Hom.: 0 Cov.: 31 AF XY: 0.00000565 AC XY: 4AN XY: 708488
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth disease Benign:1
Benign, no assertion criteria provided | research | Dept. of Medical Genetics, Telemark Hospital Trust, Telemark Hospital Trust | Oct 01, 2014 | Present in only four out of five affected family members, seen in one unaffected family member. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at