chr2-11713862-A-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001261428.3(LPIN1):c.138+50A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 1,292,316 control chromosomes in the GnomAD database, including 170,807 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001261428.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LPIN1 | NM_001261428.3 | c.138+50A>T | intron_variant | Intron 2 of 21 | NP_001248357.1 | |||
LPIN1 | NM_001349207.2 | c.81+36134A>T | intron_variant | Intron 1 of 20 | NP_001336136.1 | |||
LPIN1 | NM_001349208.2 | c.138+50A>T | intron_variant | Intron 2 of 20 | NP_001336137.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.397 AC: 60323AN: 152042Hom.: 14147 Cov.: 33
GnomAD3 exomes AF: 0.494 AC: 60640AN: 122656Hom.: 15538 AF XY: 0.504 AC XY: 33783AN XY: 67052
GnomAD4 exome AF: 0.522 AC: 594804AN: 1140156Hom.: 156659 Cov.: 15 AF XY: 0.524 AC XY: 299669AN XY: 572216
GnomAD4 genome AF: 0.396 AC: 60330AN: 152160Hom.: 14148 Cov.: 33 AF XY: 0.400 AC XY: 29718AN XY: 74376
ClinVar
Submissions by phenotype
not provided Benign:2
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. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at