14-73719459-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001367710.1(MIDEAS):c.2980C>A(p.Pro994Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001367710.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIDEAS | NM_001367710.1 | c.2980C>A | p.Pro994Thr | missense_variant | 12/13 | ENST00000423556.7 | NP_001354639.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIDEAS | ENST00000423556.7 | c.2980C>A | p.Pro994Thr | missense_variant | 12/13 | 2 | NM_001367710.1 | ENSP00000407767.2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248242Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134556
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461782Hom.: 0 Cov.: 37 AF XY: 0.0000110 AC XY: 8AN XY: 727184
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152120Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 28, 2024 | The c.2980C>A (p.P994T) alteration is located in exon 12 (coding exon 11) of the ELMSAN1 gene. This alteration results from a C to A substitution at nucleotide position 2980, causing the proline (P) at amino acid position 994 to be replaced by a threonine (T). 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