chr2-72917874-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004097.3(EMX1):c.22C>T(p.Pro8Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000542 in 1,476,442 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_004097.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EMX1 | ENST00000258106.11 | c.22C>T | p.Pro8Ser | missense_variant | Exon 1 of 3 | 1 | NM_004097.3 | ENSP00000258106.6 | ||
EMX1 | ENST00000394111.6 | c.377+814C>T | intron_variant | Intron 1 of 2 | 3 | ENSP00000482619.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151804Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000255 AC: 2AN: 78460Hom.: 0 AF XY: 0.0000446 AC XY: 2AN XY: 44834
GnomAD4 exome AF: 0.00000453 AC: 6AN: 1324638Hom.: 0 Cov.: 31 AF XY: 0.00000459 AC XY: 3AN XY: 652974
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151804Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74160
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.22C>T (p.P8S) alteration is located in exon 1 (coding exon 1) of the EMX1 gene. This alteration results from a C to T substitution at nucleotide position 22, causing the proline (P) at amino acid position 8 to be replaced by a serine (S). 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