chr2-99161958-A-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_145199.3(LIPT1):c.1A>T(p.Met1?) variant causes a initiator codon, splice region change. The variant allele was found at a frequency of 0.000282 in 1,588,848 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_145199.3 initiator_codon, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIPT1 | ENST00000651691.1 | c.1A>T | p.Met1? | initiator_codon_variant, splice_region_variant | Exon 2 of 2 | NM_145199.3 | ENSP00000498546.1 | |||
ENSG00000273155 | ENST00000410042.1 | c.-28+5532A>T | intron_variant | Intron 2 of 5 | 2 | ENSP00000387111.1 | ||||
ENSG00000241962 | ENST00000424491.5 | n.63+11439A>T | intron_variant | Intron 4 of 13 | 2 | ENSP00000390891.1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152198Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000564 AC: 134AN: 237538Hom.: 3 AF XY: 0.000860 AC XY: 111AN XY: 129144
GnomAD4 exome AF: 0.000301 AC: 433AN: 1436532Hom.: 9 Cov.: 30 AF XY: 0.000437 AC XY: 311AN XY: 712040
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152316Hom.: 0 Cov.: 31 AF XY: 0.000134 AC XY: 10AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:2
- -
LIPT1: BS2 -
LIPT1-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