chrX-70038122-G-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001399.5(EDA):c.*2513G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0844 in 111,175 control chromosomes in the GnomAD database, including 518 homozygotes. There are 2,827 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001399.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDA | NM_001399.5 | c.*2513G>C | 3_prime_UTR_variant | 8/8 | ENST00000374552.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDA | ENST00000374552.9 | c.*2513G>C | 3_prime_UTR_variant | 8/8 | 1 | NM_001399.5 | P4 | ||
EDA | ENST00000374553.6 | c.*2513G>C | 3_prime_UTR_variant | 8/8 | 1 | A1 | |||
ENST00000651174.1 | n.1045C>G | non_coding_transcript_exon_variant | 2/2 | ||||||
EDA | ENST00000616899.1 | c.*2513G>C | 3_prime_UTR_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0840 AC: 9328AN: 111089Hom.: 506 Cov.: 22 AF XY: 0.0841 AC XY: 2801AN XY: 33323
GnomAD4 exome AF: 0.0938 AC: 3AN: 32Hom.: 0 Cov.: 0 AF XY: 0.214 AC XY: 3AN XY: 14
GnomAD4 genome AF: 0.0844 AC: 9376AN: 111143Hom.: 518 Cov.: 22 AF XY: 0.0846 AC XY: 2824AN XY: 33387
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at