rs2184953
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002016.2(FLG):c.6580T>C(p.Tyr2194His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 1,613,226 control chromosomes in the GnomAD database, including 63,839 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002016.2 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 | UniProt |
---|---|---|---|---|---|---|---|
FLG | NM_002016.2 | c.6580T>C | p.Tyr2194His | missense_variant | 3/3 | ENST00000368799.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLG | ENST00000368799.2 | c.6580T>C | p.Tyr2194His | missense_variant | 3/3 | 1 | NM_002016.2 | P1 | |
FLG-AS1 | ENST00000653548.1 | n.390-24277A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.370 AC: 55897AN: 151236Hom.: 14547 Cov.: 32
GnomAD3 exomes AF: 0.319 AC: 80243AN: 251412Hom.: 17318 AF XY: 0.308 AC XY: 41832AN XY: 135878
GnomAD4 exome AF: 0.219 AC: 320538AN: 1461870Hom.: 49249 Cov.: 123 AF XY: 0.222 AC XY: 161774AN XY: 727234
GnomAD4 genome ? AF: 0.370 AC: 55989AN: 151356Hom.: 14590 Cov.: 32 AF XY: 0.376 AC XY: 27816AN XY: 73884
ClinVar
Submissions by phenotype
Ichthyosis vulgaris Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at