rs201434694
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_022336.4(EDAR):c.1017C>T(p.Val339=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,614,036 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. V339V) has been classified as Likely benign.
Frequency
Consequence
NM_022336.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDAR | NM_022336.4 | c.1017C>T | p.Val339= | synonymous_variant | 11/12 | ENST00000258443.7 | |
EDAR | XM_006712204.2 | c.1113C>T | p.Val371= | synonymous_variant | 10/11 | ||
RANBP2 | XM_047445367.1 | c.8370+133269G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDAR | ENST00000258443.7 | c.1017C>T | p.Val339= | synonymous_variant | 11/12 | 1 | NM_022336.4 | P1 | |
EDAR | ENST00000376651.1 | c.1113C>T | p.Val371= | synonymous_variant | 10/11 | 2 | |||
EDAR | ENST00000409271.5 | c.1113C>T | p.Val371= | synonymous_variant | 11/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152072Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000235 AC: 59AN: 251490Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135920
GnomAD4 exome AF: 0.000150 AC: 220AN: 1461846Hom.: 1 Cov.: 33 AF XY: 0.000151 AC XY: 110AN XY: 727228
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74390
ClinVar
Submissions by phenotype
Autosomal recessive hypohidrotic ectodermal dysplasia syndrome;C3888065:Ectodermal dysplasia 10A, hypohidrotic/hair/nail type, autosomal dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Hypohidrotic ectodermal dysplasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at