chr2-32640340-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.467C>T(p.Ser156Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,613,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTC27 | ENST00000317907.9 | c.467C>T | p.Ser156Leu | missense_variant | Exon 4 of 20 | 1 | NM_017735.5 | ENSP00000313953.4 | ||
TTC27 | ENST00000448773.5 | c.317C>T | p.Ser106Leu | missense_variant | Exon 4 of 4 | 4 | ENSP00000393327.1 | |||
TTC27 | ENST00000647819.1 | n.467C>T | non_coding_transcript_exon_variant | Exon 4 of 22 | ENSP00000497009.1 | |||||
TTC27 | ENST00000454690.1 | n.88+11960C>T | intron_variant | Intron 1 of 3 | 3 | ENSP00000392883.1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152126Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000203 AC: 51AN: 251286Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135834
GnomAD4 exome AF: 0.000176 AC: 257AN: 1461688Hom.: 0 Cov.: 31 AF XY: 0.000176 AC XY: 128AN XY: 727150
GnomAD4 genome AF: 0.000118 AC: 18AN: 152126Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 10AN XY: 74308
ClinVar
Submissions by phenotype
not specified Benign:1
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