rs16844401
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001528.4(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
NM_001528.4 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 | ENSP00000372224.4 | ||
HGFAC | ENST00000511533.1 | c.1547G>A | p.Arg516His | missense_variant | 13/15 | 1 | ENSP00000421801.1 | |||
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