rs16833974
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001014342.3(FLG2):āc.3746A>Gā(p.His1249Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0117 in 1,614,062 control chromosomes in the GnomAD database, including 1,573 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 (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001014342.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLG2 | NM_001014342.3 | c.3746A>G | p.His1249Arg | missense_variant | 3/3 | ENST00000388718.5 | |
FLG-AS1 | NR_103778.1 | n.1407-9947T>C | intron_variant, non_coding_transcript_variant | ||||
FLG-AS1 | NR_103779.1 | n.152-9947T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLG2 | ENST00000388718.5 | c.3746A>G | p.His1249Arg | missense_variant | 3/3 | 5 | NM_001014342.3 | P1 | |
FLG-AS1 | ENST00000653548.1 | n.757+15951T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0573 AC: 8715AN: 152150Hom.: 851 Cov.: 33
GnomAD3 exomes AF: 0.0162 AC: 4078AN: 251318Hom.: 330 AF XY: 0.0123 AC XY: 1664AN XY: 135824
GnomAD4 exome AF: 0.00692 AC: 10114AN: 1461794Hom.: 721 Cov.: 37 AF XY: 0.00600 AC XY: 4360AN XY: 727210
GnomAD4 genome ? AF: 0.0574 AC: 8739AN: 152268Hom.: 852 Cov.: 33 AF XY: 0.0560 AC XY: 4170AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at