rs143090653
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001375808.2(LPIN2):c.1867C>T(p.Pro623Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00158 in 1,614,160 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001375808.2 missense
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LPIN2 | NM_001375808.2 | c.1867C>T | p.Pro623Ser | missense_variant | 14/20 | ENST00000677752.1 | NP_001362737.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LPIN2 | ENST00000677752.1 | c.1867C>T | p.Pro623Ser | missense_variant | 14/20 | NM_001375808.2 | ENSP00000504857 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00809 AC: 1231AN: 152170Hom.: 20 Cov.: 32
GnomAD3 exomes AF: 0.00206 AC: 519AN: 251494Hom.: 9 AF XY: 0.00156 AC XY: 212AN XY: 135920
GnomAD4 exome AF: 0.000904 AC: 1322AN: 1461872Hom.: 20 Cov.: 32 AF XY: 0.000793 AC XY: 577AN XY: 727238
GnomAD4 genome AF: 0.00811 AC: 1235AN: 152288Hom.: 20 Cov.: 32 AF XY: 0.00767 AC XY: 571AN XY: 74458
ClinVar
Submissions by phenotype
Majeed syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 16, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 19, 2016 | 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Autoinflammatory syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | May 03, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at