chr8-133244367-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_006096.4(NDRG1):c.879G>A(p.Pro293=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000797 in 1,614,200 control chromosomes in the GnomAD database, including 11 homozygotes. 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. P293P) has been classified as Likely benign.
Frequency
Consequence
NM_006096.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDRG1 | NM_006096.4 | c.879G>A | p.Pro293= | synonymous_variant | 14/16 | ENST00000323851.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDRG1 | ENST00000323851.13 | c.879G>A | p.Pro293= | synonymous_variant | 14/16 | 1 | NM_006096.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00427 AC: 650AN: 152232Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00117 AC: 295AN: 251204Hom.: 1 AF XY: 0.000847 AC XY: 115AN XY: 135814
GnomAD4 exome AF: 0.000432 AC: 632AN: 1461850Hom.: 5 Cov.: 31 AF XY: 0.000399 AC XY: 290AN XY: 727216
GnomAD4 genome AF: 0.00430 AC: 655AN: 152350Hom.: 6 Cov.: 33 AF XY: 0.00411 AC XY: 306AN XY: 74504
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth disease type 4D Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 14, 2023 | - - |
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 13, 2019 | - - |
Charcot-Marie-Tooth disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Molecular Genetics Laboratory, London Health Sciences Centre | - | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 06, 2020 | - - |
Charcot-Marie-Tooth disease type 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at