rs121918122
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The ENST00000232003.5(HRG):c.308G>A(p.Gly103Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000141 in 1,419,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G103R) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000232003.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HRG | NM_000412.5 | c.308G>A | p.Gly103Glu | missense_variant | 3/7 | ENST00000232003.5 | NP_000403.1 | |
HRG-AS1 | XR_924801.3 | n.291-18074C>T | intron_variant, non_coding_transcript_variant | |||||
HRG | XM_005247415.5 | c.308G>A | p.Gly103Glu | missense_variant | 3/7 | XP_005247472.1 | ||
HRG-AS1 | XR_001741059.2 | n.291-18074C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HRG | ENST00000232003.5 | c.308G>A | p.Gly103Glu | missense_variant | 3/7 | 1 | NM_000412.5 | ENSP00000232003 | P1 | |
HRG-AS1 | ENST00000630178.2 | n.238+48522C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000141 AC: 2AN: 1419586Hom.: 0 Cov.: 25 AF XY: 0.00000141 AC XY: 1AN XY: 708870
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Hereditary thrombophilia due to congenital histidine-rich (poly-L) glycoprotein deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 1998 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at