chr16-69109919-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_001199280.2(HAS3):c.524G>A(p.Arg175Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,614,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001199280.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAS3 | NM_001199280.2 | c.524G>A | p.Arg175Gln | missense_variant | 2/4 | ENST00000569188.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAS3 | ENST00000569188.6 | c.524G>A | p.Arg175Gln | missense_variant | 2/4 | 2 | NM_001199280.2 | P1 | |
HAS3 | ENST00000306560.1 | c.524G>A | p.Arg175Gln | missense_variant | 2/4 | 1 | P1 | ||
HAS3 | ENST00000219322.7 | c.524G>A | p.Arg175Gln | missense_variant | 2/4 | 1 | |||
HAS3 | ENST00000566118.5 | c.524G>A | p.Arg175Gln | missense_variant | 2/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 250876Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135762
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461724Hom.: 0 Cov.: 34 AF XY: 0.0000426 AC XY: 31AN XY: 727166
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152372Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74516
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.524G>A (p.R175Q) alteration is located in exon 2 (coding exon 1) of the HAS3 gene. This alteration results from a G to A substitution at nucleotide position 524, causing the arginine (R) at amino acid position 175 to be replaced by a glutamine (Q). 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