rs7193541
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018124.4(RFWD3):āc.1690A>Gā(p.Ile564Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 1,613,106 control chromosomes in the GnomAD database, including 133,593 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_018124.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RFWD3 | NM_018124.4 | c.1690A>G | p.Ile564Val | missense_variant | 10/13 | ENST00000361070.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RFWD3 | ENST00000361070.9 | c.1690A>G | p.Ile564Val | missense_variant | 10/13 | 1 | NM_018124.4 | P1 | |
RFWD3 | ENST00000571750.5 | c.1690A>G | p.Ile564Val | missense_variant | 11/14 | 2 | P1 | ||
RFWD3 | ENST00000575154.1 | n.324A>G | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.422 AC: 64063AN: 151860Hom.: 14033 Cov.: 32
GnomAD3 exomes AF: 0.370 AC: 92839AN: 250638Hom.: 18411 AF XY: 0.367 AC XY: 49768AN XY: 135466
GnomAD4 exome AF: 0.399 AC: 583288AN: 1461126Hom.: 119551 Cov.: 41 AF XY: 0.394 AC XY: 286659AN XY: 726858
GnomAD4 genome ? AF: 0.422 AC: 64095AN: 151980Hom.: 14042 Cov.: 32 AF XY: 0.414 AC XY: 30753AN XY: 74266
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at