chr15-56094235-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP3BP6_ModerateBS2
The NM_022841.7(RFX7):c.3493C>T(p.Arg1165Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,794 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1165Q) has been classified as Likely benign.
Frequency
Consequence
NM_022841.7 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 |
---|---|---|---|---|---|---|---|
RFX7 | NM_022841.7 | c.3493C>T | p.Arg1165Trp | missense_variant | 10/10 | ENST00000559447.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RFX7 | ENST00000559447.8 | c.3493C>T | p.Arg1165Trp | missense_variant | 10/10 | 5 | NM_022841.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000482 AC: 12AN: 248830Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134956
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461670Hom.: 0 Cov.: 33 AF XY: 0.0000413 AC XY: 30AN XY: 727124
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74306
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at