NM_001366145.2:c.973+17780A>G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001366145.2(TRPM3):c.973+17780A>G variant causes a intron change. The variant allele was found at a frequency of 0.0000224 in 534,642 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_001366145.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRPM3 | NM_001366145.2 | c.973+17780A>G | intron_variant | Intron 6 of 25 | ENST00000677713.2 | NP_001353074.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRPM3 | ENST00000677713.2 | c.973+17780A>G | intron_variant | Intron 6 of 25 | NM_001366145.2 | ENSP00000503830.2 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152064Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251048Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135896
GnomAD4 exome AF: 0.0000157 AC: 6AN: 382460Hom.: 0 Cov.: 0 AF XY: 0.0000184 AC XY: 4AN XY: 217726
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152182Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74394
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant occurs in the MIR204 gene, which encodes an RNA molecule that does not result in a protein product. This variant is present in population databases (rs548588673, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with MIR204-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at