dbSNP rs3817003: NDEL1:c.944+146G>A (chr17-8460306-G-A) – 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+146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 823,174 control chromosomes in the GnomAD database, including 131,491 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 0.51 ( 20601 hom., cov: 31)

Exomes 𝑓: 0.57 ( 110890 hom. )

Consequence

NDEL1
NM_030808.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.790

Publications

13 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 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+146G>A	intron	N/A	NP_110435.1	Q9GZM8-1
NDEL1	NM_001025579.3		c.944+146G>A	intron	N/A	NP_001020750.1	Q9GZM8-3
NDEL1	NM_001330129.2		c.792+5419G>A	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+146G>A	intron	N/A	ENSP00000333982.7	Q9GZM8-1
NDEL1	ENST00000852241.1		c.945-19G>A	intron	N/A	ENSP00000522300.1
NDEL1	ENST00000852238.1		c.944+146G>A	intron	N/A	ENSP00000522297.1

Frequencies

GnomAD3 genomes

AF:

0.509

AC:

77231

AN:

151814

Hom.:

20605

Cov.:

show subpopulations

Gnomad AFR

AF:

0.321

Gnomad AMI

AF:

0.679

Gnomad AMR

AF:

0.575

Gnomad ASJ

AF:

0.666

Gnomad EAS

AF:

0.566

Gnomad SAS

AF:

0.547

Gnomad FIN

AF:

0.540

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.584

Gnomad OTH

AF:

0.552

GnomAD4 exome

AF:

0.570

AC:

382807

AN:

671242

Hom.:

110890

AF XY:

0.570

AC XY:

195653

AN XY:

342980

show subpopulations

African (AFR)

AF:

0.304

AC:

4725

AN:

15522

American (AMR)

AF:

0.589

AC:

9432

AN:

16026

Ashkenazi Jewish (ASJ)

AF:

0.652

AC:

9512

AN:

14578

East Asian (EAS)

AF:

0.629

AC:

18693

AN:

29732

South Asian (SAS)

AF:

0.552

AC:

25697

AN:

46516

European-Finnish (FIN)

AF:

0.544

AC:

19108

AN:

35138

Middle Eastern (MID)

AF:

0.602

AC:

2012

AN:

3344

European-Non Finnish (NFE)

AF:

0.577

AC:

275574

AN:

477862

Other (OTH)

AF:

0.555

AC:

18054

AN:

32524

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

7671

15343

23014

30686

38357

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5356

10712

16068

21424

26780

<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:

0.508

AC:

77240

AN:

151932

Hom.:

20601

Cov.:

AF XY:

0.508

AC XY:

37714

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.321

AC:

13305

AN:

41442

American (AMR)

AF:

0.575

AC:

8770

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.666

AC:

2308

AN:

3468

East Asian (EAS)

AF:

0.567

AC:

2919

AN:

5148

South Asian (SAS)

AF:

0.546

AC:

2629

AN:

4814

European-Finnish (FIN)

AF:

0.540

AC:

5684

AN:

10528

Middle Eastern (MID)

AF:

0.616

AC:

181

AN:

294

European-Non Finnish (NFE)

AF:

0.584

AC:

39678

AN:

67970

Other (OTH)

AF:

0.546

AC:

1151

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

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

698

1396

2094

2792

3490

<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:

0.575

Hom.:

42613

Bravo

AF:

0.502

Asia WGS

AF:

0.553

AC:

1921

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.22

(source)

DANN

Benign

0.61

PhyloP100

-0.79

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