19-19258660-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_023002.3(HAPLN4):c.680G>A(p.Arg227Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000048 in 1,458,194 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023002.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HAPLN4 | ENST00000291481.8 | c.680G>A | p.Arg227Gln | missense_variant | Exon 4 of 5 | 1 | NM_023002.3 | ENSP00000291481.5 | ||
ENSG00000267629 | ENST00000586064.3 | n.1811G>A | non_coding_transcript_exon_variant | Exon 11 of 12 | 2 | |||||
HAPLN4 | ENST00000592862.2 | n.*186G>A | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000838 AC: 2AN: 238548Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 130406
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1458194Hom.: 0 Cov.: 33 AF XY: 0.00000552 AC XY: 4AN XY: 725290
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.680G>A (p.R227Q) alteration is located in exon 4 (coding exon 4) of the HAPLN4 gene. This alteration results from a G to A substitution at nucleotide position 680, causing the arginine (R) at amino acid position 227 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