17-8473636-C-T

Variant names:

• chr17-8473636-C-T
• rs35261231
• XM_017025183.2:c.*2075C>T

Variant summary

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

The XM_017025183.2(NDEL1):​c.*2075C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,036 control chromosomes in the GnomAD database, including 12,313 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 (12313 hom., cov: 32)
• Consequence: NDEL1 XM_017025183.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581679.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDEL1	ENST00000581679.1	TSL:4	c.416+13476C>T		intron	N/A	ENSP00000464634.1

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61059 AN: 151918 Hom.: 12297 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.351

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: 0.402 AC: 61109 AN: 152036 Hom.: 12313 Cov.: 32 AF XY: 0.405 AC XY: 30070 AN XY: 74310

African (AFR) AF: 0.375 AC: 15560 AN: 41480

American (AMR) AF: 0.386 AC: 5898 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1112 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2198 AN: 5172

South Asian (SAS) AF: 0.452 AC: 2179 AN: 4818

European-Finnish (FIN) AF: 0.455 AC: 4797 AN: 10550

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28140 AN: 67958

Other (OTH) AF: 0.393 AC: 827 AN: 2104

Alfa AF: 0.396 Hom.: 15260

Bravo AF: 0.396

Asia WGS AF: 0.426 AC: 1480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.40
DANN	Benign	0.36
PhyloP100		-0.86
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs35261231; hg19: chr17-8376954;