rs931671

Positions:

• chr17-8426647-G-A
• chr17-8426647-G-C
• chr17-8426647-G-T

Variant summary

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

The ENST00000582812.5(NDEL1):​c.-13+13378G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,902 control chromosomes in the GnomAD database, including 8,894 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 0.32 (8894 hom., cov: 31)
• Consequence: NDEL1 ENST00000582812.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.892

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=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NDEL1	XM_047436861.1	c.-13+13378G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDEL1	ENST00000582812.5	c.-13+13378G>A		intron_variant		4
NDEL1	ENST00000580237.5	c.-13+13378G>A		intron_variant, NMD_transcript_variant		4
NDEL1	ENST00000579150.1	n.139-4555G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49242 AN: 151786 Hom.: 8891 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.324 AC: 49270 AN: 151902 Hom.: 8894 Cov.: 31 AF XY: 0.327 AC XY: 24220 AN XY: 74180

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.313

Alfa AF: 0.371 Hom.: 18116

Bravo AF: 0.316

Asia WGS AF: 0.343 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	10
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs931671; hg19: chr17-8329965;