17-58205983-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_017777.4(MKS1):c.*96C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000158 in 1,541,034 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_017777.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000480 AC: 73AN: 152156Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000123 AC: 171AN: 1388760Hom.: 2 Cov.: 31 AF XY: 0.000109 AC XY: 75AN XY: 685148
GnomAD4 genome AF: 0.000479 AC: 73AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74454
ClinVar
Submissions by phenotype
MKS1-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