19-51713720-T-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001297436.2(HAS1):c.1441A>C(p.Thr481Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,206 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAS1 | NM_001297436.2 | c.1441A>C | p.Thr481Pro | missense_variant | 5/5 | ENST00000540069.7 | |
HAS1 | NM_001523.4 | c.1444A>C | p.Thr482Pro | missense_variant | 5/5 | ||
HAS1 | XM_011526884.3 | c.*324A>C | 3_prime_UTR_variant | 4/4 | |||
HAS1 | XM_047438719.1 | c.*324A>C | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAS1 | ENST00000540069.7 | c.1441A>C | p.Thr481Pro | missense_variant | 5/5 | 1 | NM_001297436.2 | A1 | |
HAS1 | ENST00000601714.5 | c.1465A>C | p.Thr489Pro | missense_variant | 4/4 | 1 | |||
HAS1 | ENST00000222115.5 | c.1444A>C | p.Thr482Pro | missense_variant | 5/5 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1454466Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 723170
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.1444A>C (p.T482P) alteration is located in exon 5 (coding exon 5) of the HAS1 gene. This alteration results from a A to C substitution at nucleotide position 1444, causing the threonine (T) at amino acid position 482 to be replaced by a proline (P). 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
Publications
No publications associated with this variant yet.