rs2192206
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_002487.3(NDN):c.858C>T(p.Asp286=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 1,595,954 control chromosomes in the GnomAD database, including 36,678 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.17 ( 2925 hom., cov: 32)
Exomes 𝑓: 0.21 ( 33753 hom. )
Consequence
NDN
NM_002487.3 synonymous
NM_002487.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.354
Genes affected
NDN (HGNC:7675): (necdin, MAGE family member) This intronless gene is located in the Prader-Willi syndrome deletion region. It is an imprinted gene and is expressed exclusively from the paternal allele. Studies in mouse suggest that the protein encoded by this gene may suppress growth in postmitotic neurons. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant 15-23686360-G-A is Benign according to our data. Variant chr15-23686360-G-A is described in ClinVar as [Benign]. Clinvar id is 2796505.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.354 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDN | NM_002487.3 | c.858C>T | p.Asp286= | synonymous_variant | 1/1 | ENST00000649030.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDN | ENST00000649030.2 | c.858C>T | p.Asp286= | synonymous_variant | 1/1 | NM_002487.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.174 AC: 26484AN: 151944Hom.: 2923 Cov.: 32
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GnomAD3 exomes AF: 0.222 AC: 52973AN: 238980Hom.: 6677 AF XY: 0.219 AC XY: 28434AN XY: 129564
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GnomAD4 exome AF: 0.211 AC: 304210AN: 1443894Hom.: 33753 Cov.: 34 AF XY: 0.210 AC XY: 150468AN XY: 716100
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GnomAD4 genome ? AF: 0.174 AC: 26486AN: 152060Hom.: 2925 Cov.: 32 AF XY: 0.177 AC XY: 13124AN XY: 74306
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 02, 2023 | - - |
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