13-77918405-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001122659.3(EDNRB):c.169G>A(p.Gly57Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00634 in 1,597,292 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001122659.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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EDNRB | NM_001122659.3 | c.169G>A | p.Gly57Ser | missense_variant | Exon 1 of 7 | ENST00000646607.2 | NP_001116131.1 | |
EDNRB | NM_001201397.2 | c.439G>A | p.Gly147Ser | missense_variant | Exon 2 of 8 | NP_001188326.1 | ||
EDNRB | NM_000115.5 | c.169G>A | p.Gly57Ser | missense_variant | Exon 2 of 8 | NP_000106.1 | ||
EDNRB | NM_003991.4 | c.169G>A | p.Gly57Ser | missense_variant | Exon 1 of 7 | NP_003982.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00452 AC: 687AN: 152032Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.00513 AC: 1225AN: 238706Hom.: 9 AF XY: 0.00523 AC XY: 674AN XY: 128756
GnomAD4 exome AF: 0.00654 AC: 9444AN: 1445142Hom.: 44 Cov.: 31 AF XY: 0.00640 AC XY: 4593AN XY: 717122
GnomAD4 genome AF: 0.00452 AC: 687AN: 152150Hom.: 1 Cov.: 31 AF XY: 0.00426 AC XY: 317AN XY: 74390
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:4
This variant is associated with the following publications: (PMID: 21507037, 9760196, 8630503, 16618617, 24633486, 9721987, 9035203, 27148356, 16145050, 20031584, 16855133, 11302967, 10192234, 11471546, 8852660, 18758497, 16002759) -
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EDNRB: BP4, BS2 -
not specified Benign:3
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p.Gly147Ser in exon 2 of EDNRB: This variant is not expected to have clinical si gnificance because it has been identified in 0.9% (76/8600) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http ://evs.gs.washington.edu/EVS; dbSNP rs1801710). -
Hirschsprung disease, susceptibility to, 2 Benign:1Other:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at