2-32630694-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_017735.5(TTC27):c.260C>T(p.Thr87Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00004 in 1,598,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_017735.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC27 | NM_017735.5 | c.260C>T | p.Thr87Met | missense_variant | 2/20 | ENST00000317907.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC27 | ENST00000317907.9 | c.260C>T | p.Thr87Met | missense_variant | 2/20 | 1 | NM_017735.5 | P1 | |
TTC27 | ENST00000448773.5 | c.110C>T | p.Thr37Met | missense_variant | 2/4 | 4 | |||
TTC27 | ENST00000647819.1 | c.260C>T | p.Thr87Met | missense_variant, NMD_transcript_variant | 2/22 | ||||
TTC27 | ENST00000454690.1 | c.88+2314C>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000713 AC: 17AN: 238412Hom.: 0 AF XY: 0.0000695 AC XY: 9AN XY: 129472
GnomAD4 exome AF: 0.0000401 AC: 58AN: 1446036Hom.: 0 Cov.: 32 AF XY: 0.0000431 AC XY: 31AN XY: 719210
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74294
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at