2-108906315-G-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_022336.4(EDAR):c.1017C>A(p.Val339=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,918 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 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 -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDAR | NM_022336.4 | c.1017C>A | p.Val339= | synonymous_variant | 11/12 | ENST00000258443.7 | |
EDAR | XM_006712204.2 | c.1113C>A | p.Val371= | synonymous_variant | 10/11 | ||
RANBP2 | XM_047445367.1 | c.8370+133269G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDAR | ENST00000258443.7 | c.1017C>A | p.Val339= | synonymous_variant | 11/12 | 1 | NM_022336.4 | P1 | |
EDAR | ENST00000376651.1 | c.1113C>A | p.Val371= | synonymous_variant | 10/11 | 2 | |||
EDAR | ENST00000409271.5 | c.1113C>A | p.Val371= | synonymous_variant | 11/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152072Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251490Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135920
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461846Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 727228
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152072Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74262
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 | Sep 05, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at