chr10-44982605-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032023.4(RASSF4):c.223C>T(p.Arg75Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,613,090 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R75Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_032023.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RASSF4 | NM_032023.4 | c.223C>T | p.Arg75Trp | missense_variant | 4/11 | ENST00000340258.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASSF4 | ENST00000340258.10 | c.223C>T | p.Arg75Trp | missense_variant | 4/11 | 1 | NM_032023.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000188 AC: 47AN: 249706Hom.: 1 AF XY: 0.000163 AC XY: 22AN XY: 135104
GnomAD4 exome AF: 0.000112 AC: 163AN: 1460782Hom.: 3 Cov.: 30 AF XY: 0.000110 AC XY: 80AN XY: 726710
GnomAD4 genome AF: 0.000171 AC: 26AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2022 | The c.223C>T (p.R75W) alteration is located in exon 4 (coding exon 3) of the RASSF4 gene. This alteration results from a C to T substitution at nucleotide position 223, causing the arginine (R) at amino acid position 75 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at