19-51713470-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001297436.2(HAS1):c.1691G>A(p.Arg564Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,565,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001297436.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HAS1 | NM_001297436.2 | c.1691G>A | p.Arg564Lys | missense_variant | Exon 5 of 5 | ENST00000540069.7 | NP_001284365.1 | |
HAS1 | NM_001523.4 | c.1694G>A | p.Arg565Lys | missense_variant | Exon 5 of 5 | NP_001514.2 | ||
HAS1 | XM_011526884.3 | c.*574G>A | 3_prime_UTR_variant | Exon 4 of 4 | XP_011525186.1 | |||
HAS1 | XM_047438719.1 | c.*574G>A | 3_prime_UTR_variant | Exon 4 of 4 | XP_047294675.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HAS1 | ENST00000540069.7 | c.1691G>A | p.Arg564Lys | missense_variant | Exon 5 of 5 | 1 | NM_001297436.2 | ENSP00000445021.2 | ||
HAS1 | ENST00000601714.5 | c.1715G>A | p.Arg572Lys | missense_variant | Exon 4 of 4 | 1 | ENSP00000472821.1 | |||
HAS1 | ENST00000222115.5 | c.1694G>A | p.Arg565Lys | missense_variant | Exon 5 of 5 | 1 | ENSP00000222115.1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000635 AC: 13AN: 204836Hom.: 0 AF XY: 0.0000793 AC XY: 9AN XY: 113508
GnomAD4 exome AF: 0.000106 AC: 150AN: 1412816Hom.: 0 Cov.: 32 AF XY: 0.0000931 AC XY: 65AN XY: 698224
GnomAD4 genome AF: 0.000145 AC: 22AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1694G>A (p.R565K) alteration is located in exon 5 (coding exon 5) of the HAS1 gene. This alteration results from a G to A substitution at nucleotide position 1694, causing the arginine (R) at amino acid position 565 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at