chr17-74230995-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032646.6(TTYH2):c.410C>T(p.Ala137Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,613,778 control chromosomes in the GnomAD database, including 1 homozygotes. 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_032646.6 missense
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTYH2 | NM_032646.6 | c.410C>T | p.Ala137Val | missense_variant | 3/14 | ENST00000269346.9 | NP_116035.5 | |
TTYH2 | NM_001330453.2 | c.347C>T | p.Ala116Val | missense_variant | 3/14 | NP_001317382.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTYH2 | ENST00000269346.9 | c.410C>T | p.Ala137Val | missense_variant | 3/14 | 1 | NM_032646.6 | ENSP00000269346 | P1 | |
TTYH2 | ENST00000529107.5 | c.347C>T | p.Ala116Val | missense_variant | 3/14 | 2 | ENSP00000433089 | |||
TTYH2 | ENST00000578825.5 | n.122C>T | non_coding_transcript_exon_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251386Hom.: 1 AF XY: 0.0000662 AC XY: 9AN XY: 135858
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461468Hom.: 1 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 727040
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.410C>T (p.A137V) alteration is located in exon 3 (coding exon 3) of the TTYH2 gene. This alteration results from a C to T substitution at nucleotide position 410, causing the alanine (A) at amino acid position 137 to be replaced by a valine (V). 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