chr16-3026255-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_024339.5(THOC6):c.329G>A(p.Cys110Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000762 in 1,614,152 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 -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THOC6 | NM_024339.5 | c.329G>A | p.Cys110Tyr | missense_variant | 5/13 | ENST00000326266.13 | |
THOC6 | NM_001347704.2 | c.329G>A | p.Cys110Tyr | missense_variant | 6/14 | ||
THOC6 | NM_001347703.2 | c.257G>A | p.Cys86Tyr | missense_variant | 6/14 | ||
THOC6 | NM_001142350.3 | c.329G>A | p.Cys110Tyr | missense_variant | 5/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THOC6 | ENST00000326266.13 | c.329G>A | p.Cys110Tyr | missense_variant | 5/13 | 1 | NM_024339.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000519 AC: 79AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251392Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135888
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461868Hom.: 0 Cov.: 38 AF XY: 0.0000220 AC XY: 16AN XY: 727230
GnomAD4 genome AF: 0.000519 AC: 79AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.000470 AC XY: 35AN XY: 74468
ClinVar
Submissions by phenotype
THOC6-related developmental delay-microcephaly-facial dysmorphism syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 25, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at