chr1-152309791-G-A
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002016.2(FLG):c.5095C>T(p.Arg1699Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 1,613,668 control chromosomes in the GnomAD database, including 33,339 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1699H) has been classified as Uncertain significance.
Frequency
Consequence
NM_002016.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.157 AC: 23815AN: 151676Hom.: 3128 Cov.: 30 show subpopulations
GnomAD2 exomes AF: 0.242 AC: 60910AN: 251468 AF XY: 0.242 show subpopulations
GnomAD4 exome AF: 0.173 AC: 252819AN: 1461874Hom.: 30208 Cov.: 81 AF XY: 0.178 AC XY: 129266AN XY: 727242 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.157 AC: 23815AN: 151794Hom.: 3131 Cov.: 30 AF XY: 0.168 AC XY: 12488AN XY: 74166 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Ichthyosis vulgaris Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at