Variant rs931671 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.892

Variant links:

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]

NDEL1 links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
NDEL1	XM_047436861.1 linkuse as main transcript	c.-13+13378G>A		intron_variant			XP_047292817.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein
NDEL1	ENST00000582812.5 linkuse as main transcript	c.-13+13378G>A	intron_variant	4	ENSP00000462052
NDEL1	ENST00000580237.5 linkuse as main transcript	c.-13+13378G>A	intron_variant, NMD_transcript_variant	4	ENSP00000464154
NDEL1	ENST00000579150.1 linkuse as main transcript	n.139-4555G>A	intron_variant, non_coding_transcript_variant	4

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49242

AN:

151786

Hom.:

8891

Cov.:

show subpopulations

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.:

AF XY:

0.327

AC XY:

24220

AN XY:

74180

show subpopulations

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

DANN

Benign

0.72

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over