1-23310998-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_005826.5(HNRNPR):c.1358G>C(p.Gly453Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000211 in 1,614,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005826.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNRNPR | ENST00000302271.11 | c.1358G>C | p.Gly453Ala | missense_variant | Exon 11 of 11 | 1 | NM_005826.5 | ENSP00000304405.6 | ||
HNRNPR | ENST00000374616.7 | c.1367G>C | p.Gly456Ala | missense_variant | Exon 11 of 11 | 1 | ENSP00000363745.3 | |||
HNRNPR | ENST00000478691.5 | c.1064G>C | p.Gly355Ala | missense_variant | Exon 10 of 10 | 1 | ENSP00000474437.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 250822Hom.: 0 AF XY: 0.0000738 AC XY: 10AN XY: 135566
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461872Hom.: 0 Cov.: 33 AF XY: 0.0000261 AC XY: 19AN XY: 727232
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74344
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at