19-51713648-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001297436.2(HAS1):c.1513C>G(p.Leu505Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000178 in 1,573,070 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAS1 | NM_001297436.2 | c.1513C>G | p.Leu505Val | missense_variant | 5/5 | ENST00000540069.7 | |
HAS1 | NM_001523.4 | c.1516C>G | p.Leu506Val | missense_variant | 5/5 | ||
HAS1 | XM_011526884.3 | c.*396C>G | 3_prime_UTR_variant | 4/4 | |||
HAS1 | XM_047438719.1 | c.*396C>G | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAS1 | ENST00000540069.7 | c.1513C>G | p.Leu505Val | missense_variant | 5/5 | 1 | NM_001297436.2 | A1 | |
HAS1 | ENST00000601714.5 | c.1537C>G | p.Leu513Val | missense_variant | 4/4 | 1 | |||
HAS1 | ENST00000222115.5 | c.1516C>G | p.Leu506Val | missense_variant | 5/5 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000172 AC: 3AN: 174642Hom.: 0 AF XY: 0.0000209 AC XY: 2AN XY: 95662
GnomAD4 exome AF: 0.0000176 AC: 25AN: 1420826Hom.: 0 Cov.: 33 AF XY: 0.0000185 AC XY: 13AN XY: 703738
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2022 | The c.1516C>G (p.L506V) alteration is located in exon 5 (coding exon 5) of the HAS1 gene. This alteration results from a C to G substitution at nucleotide position 1516, causing the leucine (L) at amino acid position 506 to be replaced by a valine (V). 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