chr8-33500336-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001102401.4(TTI2):c.1414C>T(p.Arg472Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,614,032 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Uncertain significance (no stars).
Frequency
Consequence
NM_001102401.4 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 |
---|---|---|---|---|---|---|---|
TTI2 | NM_001102401.4 | c.1414C>T | p.Arg472Trp | missense_variant | 7/8 | ENST00000431156.7 | |
MAK16 | NM_032509.4 | c.*1707G>A | 3_prime_UTR_variant | 10/10 | ENST00000360128.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTI2 | ENST00000431156.7 | c.1414C>T | p.Arg472Trp | missense_variant | 7/8 | 1 | NM_001102401.4 | P1 | |
MAK16 | ENST00000360128.11 | c.*1707G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_032509.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152072Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250430Hom.: 1 AF XY: 0.000125 AC XY: 17AN XY: 135476
GnomAD4 exome AF: 0.000113 AC: 165AN: 1461842Hom.: 1 Cov.: 31 AF XY: 0.000102 AC XY: 74AN XY: 727224
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152190Hom.: 1 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74404
ClinVar
Submissions by phenotype
Microcephaly Uncertain:1
Uncertain significance, no assertion criteria provided | research | Department of Pediatrics, Samsung Medical Center, Samsung Medical Center | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at