ENST00000582812.5:c.-13+14515G>C

Variant names:

• chr17-8427784-G-C
• rs12601035
• ENST00000582812.5:c.-13+14515G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 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+14515G>C		intron	N/A	ENSP00000462052.1
	NDEL1	ENST00000579150.1	TSL:4	n.139-3418G>C		intron	N/A
	NDEL1	ENST00000580237.5	TSL:4	n.-13+14515G>C		intron	N/A	ENSP00000464154.1

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

African (AFR) AF: 0.358 AC: 14855 AN: 41442

American (AMR) AF: 0.324 AC: 4956 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1134 AN: 3472

East Asian (EAS) AF: 0.341 AC: 1768 AN: 5178

South Asian (SAS) AF: 0.348 AC: 1680 AN: 4824

European-Finnish (FIN) AF: 0.293 AC: 3099 AN: 10566

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26144 AN: 67962

Other (OTH) AF: 0.395 AC: 835 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.41
DANN	Benign	0.54
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs12601035; hg19: chr17-8331102;