chr19-51713480-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001297436.2(HAS1):c.1681G>A(p.Gly561Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000164 in 1,581,604 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAS1 | NM_001297436.2 | c.1681G>A | p.Gly561Ser | missense_variant | 5/5 | ENST00000540069.7 | |
HAS1 | NM_001523.4 | c.1684G>A | p.Gly562Ser | missense_variant | 5/5 | ||
HAS1 | XM_011526884.3 | c.*564G>A | 3_prime_UTR_variant | 4/4 | |||
HAS1 | XM_047438719.1 | c.*564G>A | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAS1 | ENST00000540069.7 | c.1681G>A | p.Gly561Ser | missense_variant | 5/5 | 1 | NM_001297436.2 | A1 | |
HAS1 | ENST00000601714.5 | c.1705G>A | p.Gly569Ser | missense_variant | 4/4 | 1 | |||
HAS1 | ENST00000222115.5 | c.1684G>A | p.Gly562Ser | missense_variant | 5/5 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000923 AC: 20AN: 216612Hom.: 0 AF XY: 0.0000334 AC XY: 4AN XY: 119900
GnomAD4 exome AF: 0.0000140 AC: 20AN: 1429254Hom.: 0 Cov.: 32 AF XY: 0.00000706 AC XY: 5AN XY: 708306
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152350Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2023 | The c.1684G>A (p.G562S) 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 1684, causing the glycine (G) at amino acid position 562 to be replaced by a serine (S). 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