chr11-113335035-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017868.4(TTC12):c.574G>A(p.Val192Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,610,260 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 18/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017868.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC12 | NM_017868.4 | c.574G>A | p.Val192Met | missense_variant, splice_region_variant | 8/22 | ENST00000529221.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC12 | ENST00000529221.6 | c.574G>A | p.Val192Met | missense_variant, splice_region_variant | 8/22 | 2 | NM_017868.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250936Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135592
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1458074Hom.: 0 Cov.: 28 AF XY: 0.00000276 AC XY: 2AN XY: 725608
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74342
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.574G>A (p.V192M) alteration is located in exon 8 (coding exon 7) of the TTC12 gene. This alteration results from a G to A substitution at nucleotide position 574, causing the valine (V) at amino acid position 192 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