rs16844401
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000382774.8(HGFAC):c.1526G>A(p.Arg509His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 1,609,362 control chromosomes in the GnomAD database, including 4,523 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000382774.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HGFAC | NM_001528.4 | c.1526G>A | p.Arg509His | missense_variant | 12/14 | ENST00000382774.8 | NP_001519.1 | |
HGFAC | NM_001297439.2 | c.1547G>A | p.Arg516His | missense_variant | 13/15 | NP_001284368.1 | ||
HGFAC | XM_047450155.1 | c.1175G>A | p.Arg392His | missense_variant | 12/14 | XP_047306111.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HGFAC | ENST00000382774.8 | c.1526G>A | p.Arg509His | missense_variant | 12/14 | 1 | NM_001528.4 | ENSP00000372224 | P2 | |
HGFAC | ENST00000511533.1 | c.1547G>A | p.Arg516His | missense_variant | 13/15 | 1 | ENSP00000421801 | A2 | ||
HGFAC | ENST00000506132.1 | n.566G>A | non_coding_transcript_exon_variant | 3/4 | 2 | |||||
HGFAC | ENST00000509689.5 | n.1436G>A | non_coding_transcript_exon_variant | 7/9 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0575 AC: 8754AN: 152182Hom.: 369 Cov.: 34
GnomAD3 exomes AF: 0.0747 AC: 18084AN: 241986Hom.: 835 AF XY: 0.0773 AC XY: 10152AN XY: 131416
GnomAD4 exome AF: 0.0698 AC: 101724AN: 1457062Hom.: 4156 Cov.: 33 AF XY: 0.0714 AC XY: 51727AN XY: 724462
GnomAD4 genome AF: 0.0574 AC: 8744AN: 152300Hom.: 367 Cov.: 34 AF XY: 0.0585 AC XY: 4359AN XY: 74452
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at