chr16-69115181-C-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_001199280.2(HAS3):c.1577C>G(p.Ala526Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000804 in 1,588,750 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001199280.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAS3 | NM_001199280.2 | c.1577C>G | p.Ala526Gly | missense_variant | 4/4 | ENST00000569188.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAS3 | ENST00000569188.6 | c.1577C>G | p.Ala526Gly | missense_variant | 4/4 | 2 | NM_001199280.2 | P1 | |
HAS3 | ENST00000306560.1 | c.1577C>G | p.Ala526Gly | missense_variant | 4/4 | 1 | P1 | ||
HAS3 | ENST00000219322.7 | c.738+1639C>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00429 AC: 653AN: 152084Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00123 AC: 281AN: 228774Hom.: 3 AF XY: 0.000913 AC XY: 112AN XY: 122614
GnomAD4 exome AF: 0.000432 AC: 621AN: 1436548Hom.: 9 Cov.: 34 AF XY: 0.000409 AC XY: 291AN XY: 711720
GnomAD4 genome ? AF: 0.00431 AC: 656AN: 152202Hom.: 8 Cov.: 32 AF XY: 0.00421 AC XY: 313AN XY: 74394
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at