dbSNP rs4791707: NDEL1:c.944+2685C>T (chr17-8462845-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_030808.5(NDEL1):c.944+2685C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 154,914 control chromosomes in the GnomAD database, including 12,061 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 11834 hom., cov: 33)

Exomes 𝑓: 0.39 ( 227 hom. )

Consequence

NDEL1
NM_030808.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0450

Publications

4 publications found

Variant links:

Genes affected

NDEL1 (HGNC:17620): (nudE neurodevelopment protein 1 like 1) Enables identical protein binding activity. Involved in chromosome segregation; positive regulation of GTPase activity; and regulation of intracellular protein transport. Located in kinetochore. Biomarker of schizophrenia. [provided by Alliance of Genome Resources, Apr 2022]

NDEL1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030808.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NDEL1	NM_030808.5	MANE Select	c.944+2685C>T	intron	N/A	NP_110435.1	Q9GZM8-1
NDEL1	NM_001025579.3		c.945-475C>T	intron	N/A	NP_001020750.1	Q9GZM8-3
NDEL1	NM_001330129.2		c.793-4085C>T	intron	N/A	NP_001317058.1	A6NIZ0

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NDEL1	ENST00000334527.12	TSL:1 MANE Select	c.944+2685C>T	intron	N/A	ENSP00000333982.7	Q9GZM8-1
NDEL1	ENST00000852241.1		c.1034+2431C>T	intron	N/A	ENSP00000522300.1
NDEL1	ENST00000852238.1		c.944+2685C>T	intron	N/A	ENSP00000522297.1

Frequencies

GnomAD3 genomes

AF:

0.394

AC:

59972

AN:

152024

Hom.:

11819

Cov.:

show subpopulations

Gnomad AFR

AF:

0.369

Gnomad AMI

AF:

0.321

Gnomad AMR

AF:

0.384

Gnomad ASJ

AF:

0.316

Gnomad EAS

AF:

0.427

Gnomad SAS

AF:

0.449

Gnomad FIN

AF:

0.431

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.406

Gnomad OTH

AF:

0.381

GnomAD4 exome

AF:

0.386

AC:

1069

AN:

2772

Hom.:

227

Cov.:

AF XY:

0.383

AC XY:

550

AN XY:

1436

show subpopulations

African (AFR)

AF:

0.278

AC:

AN:

American (AMR)

AF:

0.305

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.406

AC:

AN:

South Asian (SAS)

AF:

0.424

AC:

118

AN:

278

European-Finnish (FIN)

AF:

0.416

AC:

AN:

166

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.383

AC:

768

AN:

2004

Other (OTH)

AF:

0.390

AC:

AN:

146

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

101

134

168

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.394

AC:

60018

AN:

152142

Hom.:

11834

Cov.:

AF XY:

0.397

AC XY:

29500

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.369

AC:

15309

AN:

41500

American (AMR)

AF:

0.384

AC:

5872

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.316

AC:

1094

AN:

3464

East Asian (EAS)

AF:

0.426

AC:

2207

AN:

5176

South Asian (SAS)

AF:

0.450

AC:

2170

AN:

4824

European-Finnish (FIN)

AF:

0.431

AC:

4566

AN:

10582

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.406

AC:

27584

AN:

67990

Other (OTH)

AF:

0.388

AC:

819

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1887

3775

5662

7550

9437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

574

1148

1722

2296

2870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.399

Hom.:

2003

Bravo

AF:

0.390

Asia WGS

AF:

0.419

AC:

1458

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.9

(source)

DANN

Benign

0.73

PhyloP100

-0.045

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over