rs3817003

chr17-8460306-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NDEL1	NM_030808.5	c.944+146G>A		intron_variant		ENST00000334527.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDEL1	ENST00000334527.12	c.944+146G>A		intron_variant		1	NM_030808.5	P1

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77231 AN: 151814 Hom.: 20605 Cov.: 31

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

Gnomad4 AFR exome AF: 0.304

Gnomad4 AMR exome AF: 0.589

Gnomad4 ASJ exome AF: 0.652

Gnomad4 EAS exome AF: 0.629

Gnomad4 SAS exome AF: 0.552

Gnomad4 FIN exome AF: 0.544

Gnomad4 NFE exome AF: 0.577

Gnomad4 OTH exome AF: 0.555

GnomAD4 genome AF: 0.508 AC: 77240 AN: 151932 Hom.: 20601 Cov.: 31 AF XY: 0.508 AC XY: 37714 AN XY: 74266

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.546

Alfa AF: 0.584 Hom.: 34400

Bravo AF: 0.502

Asia WGS AF: 0.553 AC: 1921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.22
Dann	Benign	0.61
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs3817003; hg19: chr17-8363624;