chr17-8426647-G-A

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

2

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]

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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 UniProt
NDEL1XM_047436861.1 linkuse as main transcriptc.-13+13378G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NDEL1ENST00000582812.5 linkuse as main transcriptc.-13+13378G>A intron_variant 4
NDEL1ENST00000580237.5 linkuse as main transcriptc.-13+13378G>A intron_variant, NMD_transcript_variant 4
NDEL1ENST00000579150.1 linkuse as main transcriptn.139-4555G>A intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.324
AC:
49242
AN:
151786
Hom.:
8891
Cov.:
31
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.:
31
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
10
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.

Other links and lift over

dbSNP: rs931671; hg19: chr17-8329965; API