6-1312883-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033260.4(FOXQ1):c.179C>T(p.Thr60Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000889 in 1,125,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T60P) has been classified as Likely benign.
Frequency
Consequence
NM_033260.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 35
GnomAD4 exome AF: 8.89e-7 AC: 1AN: 1125196Hom.: 0 Cov.: 79 AF XY: 0.00 AC XY: 0AN XY: 540212
GnomAD4 genome Cov.: 35
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.179C>T (p.T60M) alteration is located in exon 1 (coding exon 1) of the FOXQ1 gene. This alteration results from a C to T substitution at nucleotide position 179, causing the threonine (T) at amino acid position 60 to be replaced by a methionine (M). 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