rs1391766

Variant names:

• chr17-8456185-G-C
• rs1391766
• NM_030808.5:c.792+1298G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDEL1	NM_030808.5	MANE Select	c.792+1298G>C		intron	N/A	NP_110435.1
	NDEL1	NM_001025579.3		c.792+1298G>C		intron	N/A	NP_001020750.1
	NDEL1	NM_001330129.2		c.792+1298G>C		intron	N/A	NP_001317058.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDEL1	ENST00000334527.12	TSL:1 MANE Select	c.792+1298G>C		intron	N/A	ENSP00000333982.7
	NDEL1	ENST00000852241.1		c.792+1298G>C		intron	N/A	ENSP00000522300.1
	NDEL1	ENST00000852238.1		c.792+1298G>C		intron	N/A	ENSP00000522297.1

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

African (AFR) AF: 0.371 AC: 15375 AN: 41422

American (AMR) AF: 0.386 AC: 5894 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1111 AN: 3468

East Asian (EAS) AF: 0.432 AC: 2230 AN: 5166

South Asian (SAS) AF: 0.452 AC: 2183 AN: 4826

European-Finnish (FIN) AF: 0.454 AC: 4786 AN: 10538

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28150 AN: 67960

Other (OTH) AF: 0.393 AC: 830 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.40
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1391766; hg19: chr17-8359503;