rs931672

Positions:

• chr17-8457331-C-T

Variant summary

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

The NM_030808.5(NDEL1):​c.792+2444C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,056 control chromosomes in the GnomAD database, including 20,685 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 (20685 hom., cov: 32)
• Consequence: NDEL1 NM_030808.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919

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=-0.96).
• 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.792+2444C>T		intron_variant		ENST00000334527.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDEL1	ENST00000334527.12	c.792+2444C>T		intron_variant		1	NM_030808.5	P1

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77440 AN: 151938 Hom.: 20688 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.509 AC: 77452 AN: 152056 Hom.: 20685 Cov.: 32 AF XY: 0.509 AC XY: 37842 AN XY: 74332

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.547

Alfa AF: 0.535 Hom.: 2793

Bravo AF: 0.503

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.22
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs931672; hg19: chr17-8360649;