Variant chr15-23686360-G-A details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.354

Variant links:

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]

NDN links:

Genome browser will be placed here

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 linkuse as main transcript	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 linkuse as main transcript	c.858C>T	p.Asp286=	synonymous_variant	1/1		NM_002487.3	P1

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26484

AN:

151944

Hom.:

2923

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0418

Gnomad AMI

AF:

0.222

Gnomad AMR

AF:

0.291

Gnomad ASJ

AF:

0.253

Gnomad EAS

AF:

0.368

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.179

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.186

GnomAD3 exomes

AF:

0.222

AC:

52973

AN:

238980

Hom.:

6677

AF XY:

0.219

AC XY:

28434

AN XY:

129564

show subpopulations

Gnomad AFR exome

AF:

0.0391

Gnomad AMR exome

AF:

0.295

Gnomad ASJ exome

AF:

0.248

Gnomad EAS exome

AF:

0.385

Gnomad SAS exome

AF:

0.184

Gnomad FIN exome

AF:

0.182

Gnomad NFE exome

AF:

0.213

Gnomad OTH exome

AF:

0.218

GnomAD4 exome

AF:

0.211

AC:

304210

AN:

1443894

Hom.:

33753

Cov.:

AF XY:

0.210

AC XY:

150468

AN XY:

716100

show subpopulations

Gnomad4 AFR exome

AF:

0.0333

Gnomad4 AMR exome

AF:

0.294

Gnomad4 ASJ exome

AF:

0.254

Gnomad4 EAS exome

AF:

0.360

Gnomad4 SAS exome

AF:

0.191

Gnomad4 FIN exome

AF:

0.190

Gnomad4 NFE exome

AF:

0.209

Gnomad4 OTH exome

AF:

0.210

GnomAD4 genome

AF:

0.174

AC:

26486

AN:

152060

Hom.:

2925

Cov.:

AF XY:

0.177

AC XY:

13124

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.0417

Gnomad4 AMR

AF:

0.291

Gnomad4 ASJ

AF:

0.253

Gnomad4 EAS

AF:

0.369

Gnomad4 SAS

AF:

0.184

Gnomad4 FIN

AF:

0.179

Gnomad4 NFE

AF:

0.207

Gnomad4 OTH

AF:

0.185

Alfa

AF:

0.158

Hom.:

864

Bravo

AF:

0.177

Asia WGS

AF:

0.233

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

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 02, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

9.3

DANN

Benign

0.66

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over