2-72918283-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_004097.3(EMX1):c.431C>A(p.Pro144Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000421 in 1,423,818 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004097.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EMX1 | ENST00000258106.11 | c.431C>A | p.Pro144Gln | missense_variant | Exon 1 of 3 | 1 | NM_004097.3 | ENSP00000258106.6 | ||
EMX1 | ENST00000473732.1 | c.65C>A | p.Pro22Gln | missense_variant | Exon 1 of 3 | 3 | ENSP00000446992.1 | |||
EMX1 | ENST00000394111.6 | c.377+1223C>A | intron_variant | Intron 1 of 2 | 3 | ENSP00000482619.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000509 AC: 1AN: 196620Hom.: 0 AF XY: 0.00000901 AC XY: 1AN XY: 110936
GnomAD4 exome AF: 0.00000421 AC: 6AN: 1423818Hom.: 0 Cov.: 31 AF XY: 0.00000282 AC XY: 2AN XY: 708632
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.431C>A (p.P144Q) alteration is located in exon 1 (coding exon 1) of the EMX1 gene. This alteration results from a C to A substitution at nucleotide position 431, causing the proline (P) at amino acid position 144 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