chrX-101412626-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP2
The NM_019597.5(HNRNPH2):c.638C>T(p.Pro213Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000911 in 1,097,404 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P213P) has been classified as Likely benign.
Frequency
Consequence
NM_019597.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNRNPH2 | NM_019597.5 | c.638C>T | p.Pro213Leu | missense_variant | 2/2 | ENST00000316594.6 | |
RPL36A-HNRNPH2 | NM_001199973.2 | c.*634C>T | 3_prime_UTR_variant | 5/5 | |||
HNRNPH2 | NM_001032393.3 | c.638C>T | p.Pro213Leu | missense_variant | 2/2 | ||
RPL36A-HNRNPH2 | NM_001199974.2 | c.*634C>T | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNRNPH2 | ENST00000316594.6 | c.638C>T | p.Pro213Leu | missense_variant | 2/2 | 1 | NM_019597.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1097404Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 362774
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 14, 2023 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 36711837, 37463454, 33728377) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at