chr9-127825704-T-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM1BP4_StrongBP6BS2
The NM_001114753.3(ENG):āc.680A>Gā(p.His227Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000114 in 1,582,578 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. H227H) has been classified as Likely benign.
Frequency
Consequence
NM_001114753.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENG | NM_001114753.3 | c.680A>G | p.His227Arg | missense_variant | 5/15 | ENST00000373203.9 | |
ENG | NM_000118.4 | c.680A>G | p.His227Arg | missense_variant | 5/14 | ||
ENG | NM_001278138.2 | c.134A>G | p.His45Arg | missense_variant | 5/15 | ||
ENG | NM_001406715.1 | c.680A>G | p.His227Arg | missense_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENG | ENST00000373203.9 | c.680A>G | p.His227Arg | missense_variant | 5/15 | 1 | NM_001114753.3 | P2 | |
ENG | ENST00000344849.4 | c.680A>G | p.His227Arg | missense_variant | 5/14 | 1 | A2 | ||
ENG | ENST00000480266.6 | c.134A>G | p.His45Arg | missense_variant | 5/15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150528Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000193 AC: 4AN: 207034Hom.: 0 AF XY: 0.00000873 AC XY: 1AN XY: 114552
GnomAD4 exome AF: 0.0000112 AC: 16AN: 1432050Hom.: 0 Cov.: 34 AF XY: 0.0000113 AC XY: 8AN XY: 709930
GnomAD4 genome AF: 0.0000133 AC: 2AN: 150528Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73408
ClinVar
Submissions by phenotype
Telangiectasia, hereditary hemorrhagic, type 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 08, 2021 | - - |
Hereditary hemorrhagic telangiectasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at