18-70020730-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_173630.4(RTTN):c.6038G>T(p.Cys2013Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00769 in 1,614,080 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_173630.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00540 AC: 822AN: 152226Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00661 AC: 1646AN: 248958Hom.: 17 AF XY: 0.00741 AC XY: 1000AN XY: 135028
GnomAD4 exome AF: 0.00793 AC: 11587AN: 1461736Hom.: 76 Cov.: 31 AF XY: 0.00807 AC XY: 5869AN XY: 727192
GnomAD4 genome AF: 0.00540 AC: 822AN: 152344Hom.: 4 Cov.: 32 AF XY: 0.00545 AC XY: 406AN XY: 74508
ClinVar
Submissions by phenotype
not provided Benign:4
RTTN: BP4, BS1, BS2 -
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not specified Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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RTTN-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at