chrX-100594027-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_022144.3(TNMD):c.313T>C(p.Phe105Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000183 in 1,095,803 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022144.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 21
GnomAD4 exome AF: 0.00000183 AC: 2AN: 1095803Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 361255
GnomAD4 genome Cov.: 21
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.313T>C (p.F105L) alteration is located in exon 3 (coding exon 3) of the TNMD gene. This alteration results from a T to C substitution at nucleotide position 313, causing the phenylalanine (F) at amino acid position 105 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.