rs12567958
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021817.3(HAPLN2):c.739+81C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 1,406,302 control chromosomes in the GnomAD database, including 341,969 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 0.58 ( 28488 hom., cov: 29)
Exomes 𝑓: 0.70 ( 313481 hom. )
Consequence
HAPLN2
NM_021817.3 intron
NM_021817.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.446
Genes affected
HAPLN2 (HGNC:17410): (hyaluronan and proteoglycan link protein 2) Predicted to enable hyaluronic acid binding activity. Predicted to be involved in central nervous system development and skeletal system development. Predicted to act upstream of or within establishment of blood-nerve barrier and extracellular matrix assembly. Predicted to be located in extracellular region. Predicted to be active in 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=-0.81).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAPLN2 | NM_021817.3 | c.739+81C>A | intron_variant | ENST00000255039.6 | |||
HAPLN2 | XM_011509853.3 | c.739+81C>A | intron_variant | ||||
HAPLN2 | XM_017002020.2 | c.739+81C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAPLN2 | ENST00000255039.6 | c.739+81C>A | intron_variant | 1 | NM_021817.3 | P1 | |||
HAPLN2 | ENST00000494218.1 | n.587+81C>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.580 AC: 87974AN: 151598Hom.: 28483 Cov.: 29
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GnomAD4 exome AF: 0.699 AC: 876988AN: 1254594Hom.: 313481 AF XY: 0.693 AC XY: 422634AN XY: 610258
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GnomAD4 genome ? AF: 0.580 AC: 87998AN: 151708Hom.: 28488 Cov.: 29 AF XY: 0.580 AC XY: 42942AN XY: 74092
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at