rs761776963
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP5BP4BS2
The NM_000412.5(HRG):c.271C>T(p.Pro91Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000436 in 1,605,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Consequence
NM_000412.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HRG | NM_000412.5 | c.271C>T | p.Pro91Ser | missense_variant | 2/7 | ENST00000232003.5 | |
HRG-AS1 | XR_924801.3 | n.291-17151G>A | intron_variant, non_coding_transcript_variant | ||||
HRG | XM_005247415.5 | c.271C>T | p.Pro91Ser | missense_variant | 2/7 | ||
HRG-AS1 | XR_001741059.2 | n.291-17151G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HRG | ENST00000232003.5 | c.271C>T | p.Pro91Ser | missense_variant | 2/7 | 1 | NM_000412.5 | P1 | |
HRG-AS1 | ENST00000630178.2 | n.238+49445G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251298Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135800
GnomAD4 exome AF: 0.00000413 AC: 6AN: 1452898Hom.: 0 Cov.: 29 AF XY: 0.00000829 AC XY: 6AN XY: 723476
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74322
ClinVar
Submissions by phenotype
Familial early-onset deep venous thrombosis Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Center of Vascular Surgery, The Second Affiliated Hospital of Nanchang University | - | - - |
Hereditary thrombophilia due to congenital histidine-rich (poly-L) glycoprotein deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at