chr5-170862046-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_022897.5(RANBP17):āc.13T>Cā(p.Phe5Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000775 in 1,463,894 control chromosomes in the GnomAD database, including 7 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 Benign (ā ).
Frequency
Consequence
NM_022897.5 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 |
---|---|---|---|---|---|---|---|
RANBP17 | NM_022897.5 | c.13T>C | p.Phe5Leu | missense_variant | 1/28 | ENST00000523189.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RANBP17 | ENST00000523189.6 | c.13T>C | p.Phe5Leu | missense_variant | 1/28 | 1 | NM_022897.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00407 AC: 619AN: 152070Hom.: 5 Cov.: 34
GnomAD3 exomes AF: 0.000201 AC: 14AN: 69792Hom.: 0 AF XY: 0.000149 AC XY: 6AN XY: 40402
GnomAD4 exome AF: 0.000393 AC: 515AN: 1311716Hom.: 2 Cov.: 31 AF XY: 0.000331 AC XY: 214AN XY: 646316
GnomAD4 genome AF: 0.00407 AC: 620AN: 152178Hom.: 5 Cov.: 34 AF XY: 0.00403 AC XY: 300AN XY: 74406
ClinVar
Submissions by phenotype
RANBP17-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 24, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at