1-32889180-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_002143.3(HPCA):c.282C>T(p.Arg94=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,614,128 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R94R) has been classified as Likely benign.
Frequency
Consequence
NM_002143.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HPCA | NM_002143.3 | c.282C>T | p.Arg94= | synonymous_variant | 2/4 | ENST00000373467.4 | |
HPCA | XM_005270792.4 | c.282C>T | p.Arg94= | synonymous_variant | 2/4 | ||
HPCA | XM_017001118.3 | c.282C>T | p.Arg94= | synonymous_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HPCA | ENST00000373467.4 | c.282C>T | p.Arg94= | synonymous_variant | 2/4 | 1 | NM_002143.3 | P1 | |
HPCA | ENST00000480118.5 | n.341C>T | non_coding_transcript_exon_variant | 2/3 | 5 | ||||
HPCA | ENST00000459874.5 | n.54+2665C>T | intron_variant, non_coding_transcript_variant | 2 | |||||
HPCA | ENST00000470166.5 | n.126+3061C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251440Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135904
GnomAD4 exome AF: 0.0000616 AC: 90AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.0000564 AC XY: 41AN XY: 727242
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74382
ClinVar
Submissions by phenotype
HPCA-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 13, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at