chr1-24342238-C-T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PM5PP3_StrongPP5_Moderate
The NM_198173.3(GRHL3):c.1171C>T(p.Arg391Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,756 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 pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R391H) has been classified as Pathogenic.
Frequency
Consequence
NM_198173.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152142Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249358Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134656
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459756Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726090
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74446
ClinVar
Submissions by phenotype
Van der Woude syndrome 2 Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 02, 2014 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 28, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at