chr16-15643555-AC-A
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000396355.5(NDE1):c.-535del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0111 in 324,396 control chromosomes in the GnomAD database, including 141 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.023 ( 141 hom., cov: 31)
Exomes 𝑓: 0.0010 ( 0 hom. )
Consequence
NDE1
ENST00000396355.5 5_prime_UTR
ENST00000396355.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -2.15
Genes affected
NDE1 (HGNC:17619): (nudE neurodevelopment protein 1) This gene encodes a member of the nuclear distribution E (NudE) family of proteins. The encoded protein is localized at the centrosome and interacts with other centrosome components as part of a multiprotein complex that regulates dynein function. This protein plays an essential role in microtubule organization, mitosis and neuronal migration. Mutations in this gene cause lissencephaly 4, a disorder characterized by lissencephaly, severe brain atrophy, microcephaly, and severe cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 16-15643555-AC-A is Benign according to our data. Variant chr16-15643555-AC-A is described in ClinVar as [Likely_benign]. Clinvar id is 318023.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0782 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDE1 | NM_001143979.2 | c.-535del | 5_prime_UTR_variant | 1/10 | NP_001137451.1 | |||
NDE1 | XM_006720897.5 | c.-317del | 5_prime_UTR_variant | 1/8 | XP_006720960.1 | |||
NDE1 | XM_047434258.1 | c.-317del | 5_prime_UTR_variant | 1/8 | XP_047290214.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDE1 | ENST00000396355.5 | c.-535del | 5_prime_UTR_variant | 1/10 | 1 | ENSP00000379643 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0233 AC: 3430AN: 146942Hom.: 141 Cov.: 31
GnomAD3 genomes
AF:
AC:
3430
AN:
146942
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00101 AC: 179AN: 177406Hom.: 0 Cov.: 0 AF XY: 0.000797 AC XY: 82AN XY: 102948
GnomAD4 exome
AF:
AC:
179
AN:
177406
Hom.:
Cov.:
0
AF XY:
AC XY:
82
AN XY:
102948
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0233 AC: 3432AN: 146990Hom.: 141 Cov.: 31 AF XY: 0.0229 AC XY: 1635AN XY: 71502
GnomAD4 genome
AF:
AC:
3432
AN:
146990
Hom.:
Cov.:
31
AF XY:
AC XY:
1635
AN XY:
71502
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
14
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Lissencephaly, Recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at