19-19258181-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_023002.3(HAPLN4):c.845G>A(p.Arg282Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000186 in 1,514,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023002.3 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 |
---|---|---|---|---|---|---|---|
HAPLN4 | NM_023002.3 | c.845G>A | p.Arg282Gln | missense_variant | 5/5 | ENST00000291481.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAPLN4 | ENST00000291481.8 | c.845G>A | p.Arg282Gln | missense_variant | 5/5 | 1 | NM_023002.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 15AN: 133624Hom.: 0 AF XY: 0.0000941 AC XY: 7AN XY: 74394
GnomAD4 exome AF: 0.000193 AC: 263AN: 1362682Hom.: 0 Cov.: 31 AF XY: 0.000199 AC XY: 133AN XY: 668402
GnomAD4 genome AF: 0.000125 AC: 19AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2021 | The c.845G>A (p.R282Q) alteration is located in exon 5 (coding exon 5) of the HAPLN4 gene. This alteration results from a G to A substitution at nucleotide position 845, causing the arginine (R) at amino acid position 282 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