rs17806986

Variant names:

• chr17-8426726-G-C
• rs17806986
• ENST00000582812.5:c.-13+13457G>C

Your query was ambiguous. Multiple possible variants found:

• chr17-8426726-G-C
• chr17-8426726-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000582812.5(NDEL1):​c.-13+13457G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,836 control chromosomes in the GnomAD database, including 10,818 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 0.37 (10818 hom., cov: 31)
• Consequence: NDEL1 ENST00000582812.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.881
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582812.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDEL1	ENST00000582812.5	TSL:4	c.-13+13457G>C		intron	N/A	ENSP00000462052.1
	NDEL1	ENST00000579150.1	TSL:4	n.139-4476G>C		intron	N/A
	NDEL1	ENST00000580237.5	TSL:4	n.-13+13457G>C		intron	N/A	ENSP00000464154.1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56741 AN: 151718 Hom.: 10806 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.374 AC: 56786 AN: 151836 Hom.: 10818 Cov.: 31 AF XY: 0.367 AC XY: 27242 AN XY: 74180

African (AFR) AF: 0.413 AC: 17063 AN: 41354

American (AMR) AF: 0.327 AC: 4999 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3472

East Asian (EAS) AF: 0.337 AC: 1740 AN: 5162

South Asian (SAS) AF: 0.352 AC: 1690 AN: 4804

European-Finnish (FIN) AF: 0.287 AC: 3034 AN: 10554

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25881 AN: 67910

Other (OTH) AF: 0.400 AC: 842 AN: 2104

Alfa AF: 0.359 Hom.: 1259

Bravo AF: 0.381

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.4
DANN	Benign	0.66
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs17806986; hg19: chr17-8330044;