1-156624073-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021817.3(HAPLN2):c.352G>T(p.Val118Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,468 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_021817.3 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 |
---|---|---|---|---|---|---|---|
HAPLN2 | NM_021817.3 | c.352G>T | p.Val118Leu | missense_variant | 4/7 | ENST00000255039.6 | |
HAPLN2 | XM_011509853.3 | c.352G>T | p.Val118Leu | missense_variant | 4/7 | ||
HAPLN2 | XM_017002020.2 | c.352G>T | p.Val118Leu | missense_variant | 5/8 | ||
HAPLN2 | XM_047427123.1 | c.485G>T | p.Arg162Leu | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAPLN2 | ENST00000255039.6 | c.352G>T | p.Val118Leu | missense_variant | 4/7 | 1 | NM_021817.3 | P1 | |
HAPLN2 | ENST00000456112.1 | c.352G>T | p.Val118Leu | missense_variant | 4/5 | 5 | |||
HAPLN2 | ENST00000494218.1 | n.10G>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243540Hom.: 0 AF XY: 0.00000753 AC XY: 1AN XY: 132832
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461300Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 726990
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at