6-31573020-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_000595.4(LTA):āc.192T>Cā(p.Ala64Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,234 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 (no stars).
Frequency
Consequence
NM_000595.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LTA | NM_000595.4 | c.192T>C | p.Ala64Ala | synonymous_variant | Exon 3 of 4 | ENST00000418386.3 | NP_000586.2 | |
LTA | NM_001159740.2 | c.192T>C | p.Ala64Ala | synonymous_variant | Exon 3 of 4 | NP_001153212.1 | ||
LTA | XM_047418773.1 | c.192T>C | p.Ala64Ala | synonymous_variant | Exon 5 of 6 | XP_047274729.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LTA | ENST00000418386.3 | c.192T>C | p.Ala64Ala | synonymous_variant | Exon 3 of 4 | 1 | NM_000595.4 | ENSP00000413450.2 | ||
LTA | ENST00000454783.5 | c.192T>C | p.Ala64Ala | synonymous_variant | Exon 3 of 4 | 2 | ENSP00000403495.1 | |||
LTA | ENST00000471842.1 | n.440T>C | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 | |||||
LTA | ENST00000489638.5 | n.320T>C | non_coding_transcript_exon_variant | Exon 2 of 3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151838Hom.: 0 Cov.: 29
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460396Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 726568
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151838Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 74140
ClinVar
Submissions by phenotype
LTA-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at