14-73721380-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001367710.1(MIDEAS):āc.2854A>Gā(p.Lys952Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000124 in 1,613,944 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001367710.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIDEAS | NM_001367710.1 | c.2854A>G | p.Lys952Glu | missense_variant | 11/13 | ENST00000423556.7 | NP_001354639.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIDEAS | ENST00000423556.7 | c.2854A>G | p.Lys952Glu | missense_variant | 11/13 | 2 | NM_001367710.1 | ENSP00000407767 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152060Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000109 AC: 27AN: 248588Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 134612
GnomAD4 exome AF: 0.000121 AC: 177AN: 1461766Hom.: 0 Cov.: 31 AF XY: 0.000122 AC XY: 89AN XY: 727160
GnomAD4 genome AF: 0.000151 AC: 23AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74402
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 02, 2023 | The c.2854A>G (p.K952E) alteration is located in exon 11 (coding exon 10) of the ELMSAN1 gene. This alteration results from a A to G substitution at nucleotide position 2854, causing the lysine (K) at amino acid position 952 to be replaced by a glutamic acid (E). 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