rs753429934
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM1BP4_ModerateBP6BS2
The NM_001114753.3(ENG):c.911G>A(p.Arg304Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,612,022 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R304G) has been classified as Likely benign.
Frequency
Consequence
NM_001114753.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENG | NM_001114753.3 | c.911G>A | p.Arg304Gln | missense_variant | 7/15 | ENST00000373203.9 | |
ENG | NM_000118.4 | c.911G>A | p.Arg304Gln | missense_variant | 7/14 | ||
ENG | NM_001278138.2 | c.365G>A | p.Arg122Gln | missense_variant | 7/15 | ||
ENG | NM_001406715.1 | c.911G>A | p.Arg304Gln | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENG | ENST00000373203.9 | c.911G>A | p.Arg304Gln | missense_variant | 7/15 | 1 | NM_001114753.3 | P2 | |
ENG | ENST00000344849.4 | c.911G>A | p.Arg304Gln | missense_variant | 7/14 | 1 | A2 | ||
ENG | ENST00000480266.6 | c.365G>A | p.Arg122Gln | missense_variant | 7/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152024Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249074Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134852
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1459998Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 726312
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152024Hom.: 0 Cov.: 28 AF XY: 0.0000539 AC XY: 4AN XY: 74254
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 08, 2022 | BP4 - |
Hereditary hemorrhagic telangiectasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 07, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at