5-170253135-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005565.5(LCP2):c.1229C>G(p.Ser410Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0162 in 1,609,648 control chromosomes in the GnomAD database, including 263 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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_005565.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0117 AC: 1775AN: 152166Hom.: 18 Cov.: 33
GnomAD3 exomes AF: 0.0122 AC: 2980AN: 244384Hom.: 24 AF XY: 0.0122 AC XY: 1619AN XY: 132346
GnomAD4 exome AF: 0.0167 AC: 24363AN: 1457364Hom.: 245 Cov.: 29 AF XY: 0.0165 AC XY: 11936AN XY: 724726
GnomAD4 genome AF: 0.0117 AC: 1775AN: 152284Hom.: 18 Cov.: 33 AF XY: 0.0108 AC XY: 806AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:1
LCP2: BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at