rs779786023
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_178518.3(TMEM102):c.235C>A(p.Pro79Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,611,522 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P79S) has been classified 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 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM102 | ENST00000323206.2 | c.235C>A | p.Pro79Thr | missense_variant | Exon 3 of 3 | 1 | NM_178518.3 | ENSP00000315387.1 | ||
ENSG00000286007 | ENST00000651314.1 | n.*123C>A | non_coding_transcript_exon_variant | Exon 4 of 4 | ENSP00000498964.1 | |||||
ENSG00000286007 | ENST00000651314.1 | n.*123C>A | 3_prime_UTR_variant | Exon 4 of 4 | ENSP00000498964.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249032Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135046
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459332Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 725662
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74342
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at