rs200268937
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_024339.5(THOC6):c.206T>C(p.Val69Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0001 in 1,614,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024339.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
THOC6 | NM_024339.5 | c.206T>C | p.Val69Ala | missense_variant | Exon 3 of 13 | ENST00000326266.13 | NP_077315.2 | |
THOC6 | NM_001347704.2 | c.206T>C | p.Val69Ala | missense_variant | Exon 4 of 14 | NP_001334633.1 | ||
THOC6 | NM_001347703.2 | c.134T>C | p.Val45Ala | missense_variant | Exon 4 of 14 | NP_001334632.1 | ||
THOC6 | NM_001142350.3 | c.206T>C | p.Val69Ala | missense_variant | Exon 3 of 12 | NP_001135822.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251488Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135918
GnomAD4 exome AF: 0.000105 AC: 154AN: 1461886Hom.: 0 Cov.: 36 AF XY: 0.000111 AC XY: 81AN XY: 727244
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74492
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.206T>C (p.V69A) alteration is located in exon 3 (coding exon 3) of the THOC6 gene. This alteration results from a T to C substitution at nucleotide position 206, causing the valine (V) at amino acid position 69 to be replaced by an alanine (A). 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