17-8427784-G-C

Position:

• chr17-8427784-G-C

Variant summary

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

The ENST00000582812.5(NDEL1):​c.-13+14515G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,042 control chromosomes in the GnomAD database, including 10,091 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 0.36 (10091 hom., cov: 32)
• Consequence: NDEL1 ENST00000582812.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NDEL1	XM_047436861.1	c.-13+14515G>C		intron_variant			XP_047292817.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDEL1	ENST00000582812.5	c.-13+14515G>C		intron_variant		4		ENSP00000462052
NDEL1	ENST00000580237.5	c.-13+14515G>C		intron_variant, NMD_transcript_variant		4		ENSP00000464154
NDEL1	ENST00000579150.1	n.139-3418G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54902 AN: 151920 Hom.: 10084 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.361 AC: 54928 AN: 152042 Hom.: 10091 Cov.: 32 AF XY: 0.355 AC XY: 26404 AN XY: 74316

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.395

Alfa AF: 0.195 Hom.: 384

Bravo AF: 0.365

Asia WGS AF: 0.347 AC: 1209 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.41
DANN	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12601035; hg19: chr17-8331102;