NM_002298.5:c.1630C>G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002298.5(LCP1):c.1630C>G(p.Pro544Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,597,352 control chromosomes in the GnomAD database, including 20 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 (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_002298.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LCP1 | NM_002298.5 | c.1630C>G | p.Pro544Ala | missense_variant | Exon 15 of 16 | ENST00000323076.7 | NP_002289.2 | |
LCP1 | XM_005266374.3 | c.1630C>G | p.Pro544Ala | missense_variant | Exon 15 of 16 | XP_005266431.1 | ||
LCP1 | XM_047430303.1 | c.1630C>G | p.Pro544Ala | missense_variant | Exon 15 of 16 | XP_047286259.1 | ||
LCP1 | XM_047430304.1 | c.1195C>G | p.Pro399Ala | missense_variant | Exon 13 of 14 | XP_047286260.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LCP1 | ENST00000323076.7 | c.1630C>G | p.Pro544Ala | missense_variant | Exon 15 of 16 | 1 | NM_002298.5 | ENSP00000315757.2 | ||
LCP1 | ENST00000398576.6 | c.1630C>G | p.Pro544Ala | missense_variant | Exon 18 of 19 | 5 | ENSP00000381581.1 | |||
LCP1 | ENST00000674665.1 | c.337C>G | p.Pro113Ala | missense_variant | Exon 4 of 5 | ENSP00000501964.1 | ||||
CPB2-AS1 | ENST00000663159.1 | n.470-20559G>C | intron_variant | Intron 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.00602 AC: 916AN: 152076Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00161 AC: 381AN: 236016Hom.: 4 AF XY: 0.00108 AC XY: 138AN XY: 128000
GnomAD4 exome AF: 0.000711 AC: 1028AN: 1445158Hom.: 11 Cov.: 31 AF XY: 0.000605 AC XY: 435AN XY: 718474
GnomAD4 genome AF: 0.00604 AC: 919AN: 152194Hom.: 9 Cov.: 32 AF XY: 0.00585 AC XY: 435AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at