5-160049615-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003314.3(TTC1):āc.643A>Gā(p.Ile215Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,606,966 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 Uncertain significance (ā ).
Frequency
Consequence
NM_003314.3 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 | UniProt |
---|---|---|---|---|---|---|---|
TTC1 | NM_003314.3 | c.643A>G | p.Ile215Val | missense_variant | 6/8 | ENST00000231238.10 | |
TTC1 | NM_001282500.2 | c.643A>G | p.Ile215Val | missense_variant | 6/8 | ||
PWWP2A | XM_011534424.4 | c.1567-4356T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC1 | ENST00000231238.10 | c.643A>G | p.Ile215Val | missense_variant | 6/8 | 1 | NM_003314.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152066Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000247 AC: 6AN: 243158Hom.: 0 AF XY: 0.0000228 AC XY: 3AN XY: 131732
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1454900Hom.: 0 Cov.: 30 AF XY: 0.0000152 AC XY: 11AN XY: 723600
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152066Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 12, 2023 | The c.643A>G (p.I215V) alteration is located in exon 6 (coding exon 5) of the TTC1 gene. This alteration results from a A to G substitution at nucleotide position 643, causing the isoleucine (I) at amino acid position 215 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