rs2192206
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_002487.3(NDN):c.858C>T(p.Asp286Asp) 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 was made for transcript
Our verdict: Benign. The variant received -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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.174 AC: 26484AN: 151944Hom.: 2923 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
26484
AN:
151944
Hom.:
Cov.:
32
Gnomad AFR
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GnomAD2 exomes AF: 0.222 AC: 52973AN: 238980 AF XY: 0.219 show subpopulations
GnomAD2 exomes
AF:
AC:
52973
AN:
238980
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.211 AC: 304210AN: 1443894Hom.: 33753 Cov.: 34 AF XY: 0.210 AC XY: 150468AN XY: 716100 show subpopulations
GnomAD4 exome
AF:
AC:
304210
AN:
1443894
Hom.:
Cov.:
34
AF XY:
AC XY:
150468
AN XY:
716100
Gnomad4 AFR exome
AF:
AC:
1095
AN:
32884
Gnomad4 AMR exome
AF:
AC:
12641
AN:
43008
Gnomad4 ASJ exome
AF:
AC:
6352
AN:
25050
Gnomad4 EAS exome
AF:
AC:
14209
AN:
39468
Gnomad4 SAS exome
AF:
AC:
15981
AN:
83758
Gnomad4 FIN exome
AF:
AC:
9972
AN:
52554
Gnomad4 NFE exome
AF:
AC:
230197
AN:
1102518
Gnomad4 Remaining exome
AF:
AC:
12509
AN:
59472
Heterozygous variant carriers
0
14687
29374
44061
58748
73435
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
8086
16172
24258
32344
40430
<30
30-35
35-40
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>80
Age
GnomAD4 genome AF: 0.174 AC: 26486AN: 152060Hom.: 2925 Cov.: 32 AF XY: 0.177 AC XY: 13124AN XY: 74306 show subpopulations
GnomAD4 genome
AF:
AC:
26486
AN:
152060
Hom.:
Cov.:
32
AF XY:
AC XY:
13124
AN XY:
74306
Gnomad4 AFR
AF:
AC:
0.0416787
AN:
0.0416787
Gnomad4 AMR
AF:
AC:
0.291481
AN:
0.291481
Gnomad4 ASJ
AF:
AC:
0.253168
AN:
0.253168
Gnomad4 EAS
AF:
AC:
0.369099
AN:
0.369099
Gnomad4 SAS
AF:
AC:
0.183673
AN:
0.183673
Gnomad4 FIN
AF:
AC:
0.178517
AN:
0.178517
Gnomad4 NFE
AF:
AC:
0.207202
AN:
0.207202
Gnomad4 OTH
AF:
AC:
0.185484
AN:
0.185484
Heterozygous variant carriers
0
1070
2140
3209
4279
5349
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
288
576
864
1152
1440
<30
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35-40
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
812
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 02, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at