rs77132068
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001122659.3(EDNRB):c.778G>T(p.Val260Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00152 in 1,612,630 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V260I) has been classified as Likely benign.
Frequency
Consequence
NM_001122659.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EDNRB | NM_001122659.3 | c.778G>T | p.Val260Phe | missense_variant | 3/7 | ENST00000646607.2 | |
EDNRB-AS1 | NR_103853.1 | n.1695-4513C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EDNRB | ENST00000646607.2 | c.778G>T | p.Val260Phe | missense_variant | 3/7 | NM_001122659.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00118 AC: 179AN: 151734Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000845 AC: 212AN: 250858Hom.: 2 AF XY: 0.000892 AC XY: 121AN XY: 135596
GnomAD4 exome AF: 0.00156 AC: 2273AN: 1460778Hom.: 2 Cov.: 32 AF XY: 0.00148 AC XY: 1079AN XY: 726724
GnomAD4 genome ? AF: 0.00118 AC: 179AN: 151852Hom.: 0 Cov.: 32 AF XY: 0.00119 AC XY: 88AN XY: 74216
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 10, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 02, 2021 | This variant is associated with the following publications: (PMID: 20127975, 17223014, 16145050) - |
ABCD syndrome;C1838564:Hirschsprung disease, susceptibility to, 2;C1848519:Waardenburg syndrome type 4A Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at