chrX-66605180-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021783.5(EDA2R):c.134C>T(p.Pro45Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000745 in 1,207,947 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P45P) has been classified as Likely benign.
Frequency
Consequence
NM_021783.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDA2R | NM_021783.5 | c.134C>T | p.Pro45Leu | missense_variant | 3/7 | ENST00000374719.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDA2R | ENST00000374719.8 | c.134C>T | p.Pro45Leu | missense_variant | 3/7 | 1 | NM_021783.5 | P1 | |
EDA2R | ENST00000253392.5 | c.134C>T | p.Pro45Leu | missense_variant | 2/6 | 1 | |||
EDA2R | ENST00000396050.5 | c.134C>T | p.Pro45Leu | missense_variant | 2/7 | 5 | |||
EDA2R | ENST00000451436.6 | c.134C>T | p.Pro45Leu | missense_variant | 3/7 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000269 AC: 3AN: 111704Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33862
GnomAD3 exomes AF: 0.0000112 AC: 2AN: 177790Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 62956
GnomAD4 exome AF: 0.00000547 AC: 6AN: 1096243Hom.: 0 Cov.: 32 AF XY: 0.00000276 AC XY: 1AN XY: 361879
GnomAD4 genome AF: 0.0000269 AC: 3AN: 111704Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33862
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.134C>T (p.P45L) alteration is located in exon 2 (coding exon 2) of the EDA2R gene. This alteration results from a C to T substitution at nucleotide position 134, causing the proline (P) at amino acid position 45 to be replaced by a leucine (L). 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