rs336963
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001884.4(HAPLN1):c.-26-336C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 215,010 control chromosomes in the GnomAD database, including 13,147 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.34 ( 9160 hom., cov: 33)
Exomes 𝑓: 0.34 ( 3987 hom. )
Consequence
HAPLN1
NM_001884.4 intron
NM_001884.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0970
Genes affected
HAPLN1 (HGNC:2380): (hyaluronan and proteoglycan link protein 1) Predicted to enable hyaluronic acid binding activity. Predicted to be an extracellular matrix structural constituent conferring compression resistance. Predicted to be involved in central nervous system development and skeletal system development. Colocalizes with collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HAPLN1 | NM_001884.4 | c.-26-336C>T | intron_variant | ENST00000274341.9 | NP_001875.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HAPLN1 | ENST00000274341.9 | c.-26-336C>T | intron_variant | 1 | NM_001884.4 | ENSP00000274341.4 |
Frequencies
GnomAD3 genomes AF: 0.343 AC: 52157AN: 152008Hom.: 9155 Cov.: 33
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GnomAD4 exome AF: 0.344 AC: 21634AN: 62884Hom.: 3987 AF XY: 0.350 AC XY: 11319AN XY: 32338
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GnomAD4 genome AF: 0.343 AC: 52193AN: 152126Hom.: 9160 Cov.: 33 AF XY: 0.345 AC XY: 25641AN XY: 74380
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at