chr19-51716274-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001297436.2(HAS1):c.1040G>C(p.Ser347Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,461,570 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 Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAS1 | NM_001297436.2 | c.1040G>C | p.Ser347Thr | missense_variant | 4/5 | ENST00000540069.7 | |
HAS1 | NM_001523.4 | c.1043G>C | p.Ser348Thr | missense_variant | 4/5 | ||
HAS1 | XM_011526884.3 | c.928+694G>C | intron_variant | ||||
HAS1 | XM_047438719.1 | c.925+694G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAS1 | ENST00000540069.7 | c.1040G>C | p.Ser347Thr | missense_variant | 4/5 | 1 | NM_001297436.2 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461570Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727110
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2022 | The c.1043G>C (p.S348T) alteration is located in exon 4 (coding exon 4) of the HAS1 gene. This alteration results from a G to C substitution at nucleotide position 1043, causing the serine (S) at amino acid position 348 to be replaced by a threonine (T). 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.