rs1391766

chr17-8456185-G-C

Variant summary

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

The NM_030808.5(NDEL1):c.792+1298G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,958 control chromosomes in the GnomAD database, including 12,231 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 0.40 (12231 hom., cov: 32)
• Consequence: NDEL1 NM_030808.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NDEL1	NM_030808.5	c.792+1298G>C		intron_variant		ENST00000334527.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDEL1	ENST00000334527.12	c.792+1298G>C		intron_variant		1	NM_030808.5	P1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60909 AN: 151838 Hom.: 12217 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.386

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.401 AC: 60956 AN: 151958 Hom.: 12231 Cov.: 32 AF XY: 0.404 AC XY: 29992 AN XY: 74270

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.393

Alfa AF: 0.411 Hom.: 1610

Bravo AF: 0.395

Asia WGS AF: 0.421 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.8
Dann	Benign	0.40

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: rs1391766; hg19: chr17-8359503;