NM_000534.5:c.418+78G>A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_000534.5(PMS1):c.418+78G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000269 in 1,582,372 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_000534.5 intron
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: 0.000560 AC: 85AN: 151698Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000291 AC: 58AN: 199036Hom.: 2 AF XY: 0.000261 AC XY: 28AN XY: 107414
GnomAD4 exome AF: 0.000237 AC: 339AN: 1430564Hom.: 2 Cov.: 33 AF XY: 0.000268 AC XY: 190AN XY: 709074
GnomAD4 genome AF: 0.000567 AC: 86AN: 151808Hom.: 0 Cov.: 33 AF XY: 0.000553 AC XY: 41AN XY: 74178
ClinVar
Submissions by phenotype
PMS1-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). -
not specified Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at