rs12964776
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000400345.8(NEDD4L):c.2752+6C>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 1,573,436 control chromosomes in the GnomAD database, including 207 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.011 ( 17 hom., cov: 32)
Exomes 𝑓: 0.013 ( 190 hom. )
Consequence
NEDD4L
ENST00000400345.8 splice_donor_region, intron
ENST00000400345.8 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.0001561
2
Clinical Significance
Conservation
PhyloP100: -0.405
Genes affected
NEDD4L (HGNC:7728): (NEDD4 like E3 ubiquitin protein ligase) This gene encodes a member of the Nedd4 family of HECT domain E3 ubiquitin ligases. HECT domain E3 ubiquitin ligases transfer ubiquitin from E2 ubiquitin-conjugating enzymes to protein substrates, thus targeting specific proteins for lysosomal degradation. The encoded protein mediates the ubiquitination of multiple target substrates and plays a critical role in epithelial sodium transport by regulating the cell surface expression of the epithelial sodium channel, ENaC. Single nucleotide polymorphisms in this gene may be associated with essential hypertension. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 18-58390748-C-T is Benign according to our data. Variant chr18-58390748-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 241027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-58390748-C-T is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.011 (1668/152240) while in subpopulation SAS AF= 0.032 (154/4816). AF 95% confidence interval is 0.0279. There are 17 homozygotes in gnomad4. There are 876 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1668 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEDD4L | NM_001144967.3 | c.2752+6C>T | splice_donor_region_variant, intron_variant | ENST00000400345.8 | NP_001138439.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEDD4L | ENST00000400345.8 | c.2752+6C>T | splice_donor_region_variant, intron_variant | 1 | NM_001144967.3 | ENSP00000383199 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0110 AC: 1669AN: 152122Hom.: 17 Cov.: 32
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GnomAD3 exomes AF: 0.0139 AC: 2810AN: 202232Hom.: 39 AF XY: 0.0153 AC XY: 1655AN XY: 107886
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GnomAD4 exome AF: 0.0133 AC: 18966AN: 1421196Hom.: 190 Cov.: 26 AF XY: 0.0142 AC XY: 9980AN XY: 704514
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GnomAD4 genome AF: 0.0110 AC: 1668AN: 152240Hom.: 17 Cov.: 32 AF XY: 0.0118 AC XY: 876AN XY: 74438
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 07, 2019 | - - |
NEDD4L-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 23, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Periventricular nodular heterotopia 7 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 13, 2021 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at