chr16-74623954-T-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_018124.4(RFWD3):c.2299A>G(p.Met767Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000697 in 1,614,118 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_018124.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RFWD3 | NM_018124.4 | c.2299A>G | p.Met767Val | missense_variant | 13/13 | ENST00000361070.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RFWD3 | ENST00000361070.9 | c.2299A>G | p.Met767Val | missense_variant | 13/13 | 1 | NM_018124.4 | P1 | |
RFWD3 | ENST00000571750.5 | c.2299A>G | p.Met767Val | missense_variant | 14/14 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000526 AC: 80AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000708 AC: 178AN: 251400Hom.: 2 AF XY: 0.000898 AC XY: 122AN XY: 135862
GnomAD4 exome AF: 0.000714 AC: 1044AN: 1461872Hom.: 4 Cov.: 31 AF XY: 0.000781 AC XY: 568AN XY: 727240
GnomAD4 genome ? AF: 0.000532 AC: 81AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.000484 AC XY: 36AN XY: 74442
ClinVar
Submissions by phenotype
RFWD3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 11, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at