17-7436896-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178518.3(TMEM102):c.917C>T(p.Thr306Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000398 in 1,609,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178518.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM102 | ENST00000323206.2 | c.917C>T | p.Thr306Ile | missense_variant | Exon 3 of 3 | 1 | NM_178518.3 | ENSP00000315387.1 | ||
TMEM102 | ENST00000396568.1 | c.917C>T | p.Thr306Ile | missense_variant | Exon 2 of 2 | 2 | ENSP00000379815.1 | |||
ENSG00000262624 | ENST00000570444.1 | n.250-262G>A | intron_variant | Intron 1 of 1 | 3 | |||||
ENSG00000262880 | ENST00000575310.1 | n.273-4575C>T | intron_variant | Intron 3 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152266Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000136 AC: 33AN: 242602Hom.: 0 AF XY: 0.0000680 AC XY: 9AN XY: 132440
GnomAD4 exome AF: 0.0000384 AC: 56AN: 1457430Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 725252
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152384Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74520
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.917C>T (p.T306I) alteration is located in exon 3 (coding exon 2) of the TMEM102 gene. This alteration results from a C to T substitution at nucleotide position 917, causing the threonine (T) at amino acid position 306 to be replaced by an isoleucine (I). 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