1-152311948-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002016.2(FLG):āc.2938C>Gā(p.His980Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0255 in 1,577,942 control chromosomes in the GnomAD database, including 708 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
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.2938C>G | p.His980Asp | missense_variant | 3/3 | ENST00000368799.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLG | ENST00000368799.2 | c.2938C>G | p.His980Asp | missense_variant | 3/3 | 1 | NM_002016.2 | P1 | |
FLG-AS1 | ENST00000653548.1 | n.390-20635G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0251 AC: 3449AN: 137672Hom.: 52 Cov.: 30
GnomAD3 exomes AF: 0.0236 AC: 5885AN: 249840Hom.: 106 AF XY: 0.0255 AC XY: 3454AN XY: 135198
GnomAD4 exome AF: 0.0255 AC: 36725AN: 1440190Hom.: 656 Cov.: 114 AF XY: 0.0266 AC XY: 19040AN XY: 716578
GnomAD4 genome AF: 0.0250 AC: 3447AN: 137752Hom.: 52 Cov.: 30 AF XY: 0.0255 AC XY: 1709AN XY: 67010
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Gene associated with ichthyosis/dermatitis - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2018 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Ichthyosis vulgaris Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at