rs754360926
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001316772.1(GARS1):c.-19C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00002 in 1,550,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001316772.1 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GARS1 | NM_002047.4 | c.144C>T | p.Ala48Ala | synonymous_variant | Exon 1 of 17 | ENST00000389266.8 | NP_002038.2 | |
GARS1 | NM_001316772.1 | c.-19C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 17 | NP_001303701.1 | |||
GARS1 | NM_001316772.1 | c.-19C>T | 5_prime_UTR_variant | Exon 1 of 17 | NP_001303701.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GARS1 | ENST00000389266.8 | c.144C>T | p.Ala48Ala | synonymous_variant | Exon 1 of 17 | 1 | NM_002047.4 | ENSP00000373918.3 | ||
GARS1 | ENST00000675651.1 | c.144C>T | p.Ala48Ala | synonymous_variant | Exon 1 of 17 | ENSP00000502513.1 | ||||
GARS1 | ENST00000675810.1 | c.144C>T | p.Ala48Ala | synonymous_variant | Exon 1 of 16 | ENSP00000502743.1 | ||||
GARS1 | ENST00000675693.1 | c.19-43C>T | intron_variant | Intron 1 of 17 | ENSP00000502174.1 | |||||
GARS1 | ENST00000675051.1 | c.22-3731C>T | intron_variant | Intron 1 of 16 | ENSP00000502296.1 | |||||
GARS1 | ENST00000674815.1 | c.-148+113C>T | intron_variant | Intron 1 of 16 | ENSP00000502799.1 | |||||
GARS1 | ENST00000674851.1 | c.-183-43C>T | intron_variant | Intron 1 of 17 | ENSP00000502451.1 | |||||
GARS1 | ENST00000444666.6 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 18 | 3 | ENSP00000415447.2 | ||||
GARS1 | ENST00000674616.1 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 18 | ENSP00000502408.1 | |||||
GARS1 | ENST00000674643.1 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 17 | ENSP00000501636.1 | |||||
GARS1 | ENST00000674737.1 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 18 | ENSP00000502464.1 | |||||
GARS1 | ENST00000674807.1 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 16 | ENSP00000502814.1 | |||||
GARS1 | ENST00000675529.1 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 18 | ENSP00000501655.1 | |||||
GARS1 | ENST00000675859.1 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 15 | ENSP00000502033.1 | |||||
GARS1 | ENST00000676088.1 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 19 | ENSP00000501884.1 | |||||
GARS1 | ENST00000676140.1 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 17 | ENSP00000502571.1 | |||||
GARS1 | ENST00000676164.1 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 17 | ENSP00000501986.1 | |||||
GARS1 | ENST00000676210.1 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 18 | ENSP00000502373.1 | |||||
GARS1 | ENST00000676259.1 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 17 | ENSP00000501980.1 | |||||
GARS1 | ENST00000676403.1 | n.144C>T | non_coding_transcript_exon_variant | Exon 1 of 16 | ENSP00000502681.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000980 AC: 15AN: 153122Hom.: 0 AF XY: 0.000108 AC XY: 9AN XY: 83706
GnomAD4 exome AF: 0.0000186 AC: 26AN: 1398396Hom.: 0 Cov.: 36 AF XY: 0.0000130 AC XY: 9AN XY: 691628
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74358
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Charcot-Marie-Tooth disease type 2 Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at