rs1801708
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001957.4(EDNRA):c.-230G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,706 control chromosomes in the GnomAD database, including 20,327 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as protective (no stars).
Frequency
Genomes: 𝑓 0.46 ( 20282 hom., cov: 32)
Exomes 𝑓: 0.39 ( 45 hom. )
Consequence
EDNRA
NM_001957.4 5_prime_UTR
NM_001957.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.56
Genes affected
EDNRA (HGNC:3179): (endothelin receptor type A) This gene encodes the receptor for endothelin-1, a peptide that plays a role in potent and long-lasting vasoconstriction. This receptor associates with guanine-nucleotide-binding (G) proteins, and this coupling activates a phosphatidylinositol-calcium second messenger system. Polymorphisms in this gene have been linked to migraine headache resistance. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 4-147481217-G-A is Benign according to our data. Variant chr4-147481217-G-A is described in ClinVar as [protective]. Clinvar id is 16642.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_benign, oryginal submission is: [protective].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDNRA | NM_001957.4 | c.-230G>A | 5_prime_UTR_variant | 1/8 | ENST00000651419.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDNRA | ENST00000651419.1 | c.-230G>A | 5_prime_UTR_variant | 1/8 | NM_001957.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.455 AC: 69175AN: 151974Hom.: 20229 Cov.: 32
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GnomAD4 exome AF: 0.390 AC: 240AN: 616Hom.: 45 Cov.: 0 AF XY: 0.384 AC XY: 132AN XY: 344
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GnomAD4 genome ? AF: 0.456 AC: 69289AN: 152090Hom.: 20282 Cov.: 32 AF XY: 0.449 AC XY: 33403AN XY: 74340
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ClinVar
Significance: protective
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Migraine, resistance to Benign:1
protective, no assertion criteria provided | literature only | OMIM | May 22, 2001 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at