NM_178518.3:c.41C>A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_178518.3(TMEM102):c.41C>A(p.Pro14Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,458,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict 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 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM102 | ENST00000323206.2 | c.41C>A | p.Pro14Gln | missense_variant | Exon 2 of 3 | 1 | NM_178518.3 | ENSP00000315387.1 | ||
ENSG00000286007 | ENST00000651314.1 | n.256C>A | non_coding_transcript_exon_variant | Exon 3 of 4 | ENSP00000498964.1 | |||||
TMEM102 | ENST00000396568.1 | c.41C>A | p.Pro14Gln | missense_variant | Exon 1 of 2 | 2 | ENSP00000379815.1 | |||
ENSG00000262880 | ENST00000575310.1 | n.273-5559C>A | intron_variant | Intron 3 of 5 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000819 AC: 2AN: 244306Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133552
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1458050Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 725082
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.41C>A (p.P14Q) alteration is located in exon 2 (coding exon 1) of the TMEM102 gene. This alteration results from a C to A substitution at nucleotide position 41, causing the proline (P) at amino acid position 14 to be replaced by a glutamine (Q). 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