rs778561832
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001114753.3(ENG):c.1434A>T(p.Arg478Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001114753.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENG | NM_001114753.3 | c.1434A>T | p.Arg478Ser | missense_variant | 12/15 | ENST00000373203.9 | |
LOC102723566 | NR_136302.1 | n.1439T>A | non_coding_transcript_exon_variant | 3/6 | |||
ENG | NM_000118.4 | c.1434A>T | p.Arg478Ser | missense_variant | 12/14 | ||
ENG | NM_001278138.2 | c.888A>T | p.Arg296Ser | missense_variant | 12/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENG | ENST00000373203.9 | c.1434A>T | p.Arg478Ser | missense_variant | 12/15 | 1 | NM_001114753.3 | P2 | |
ENST00000439298.5 | n.1439T>A | non_coding_transcript_exon_variant | 3/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248242Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134512
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461220Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726864
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Hereditary hemorrhagic telangiectasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at