rs41308365

Positions:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_018136.5(ASPM):c.7674C>T(p.Ile2558=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 1,607,148 control chromosomes in the GnomAD database, including 128,815 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. I2558I) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.30 ( 8698 hom., cov: 32)

Exomes 𝑓: 0.40 ( 120117 hom. )

Consequence

ASPM
NM_018136.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11O:1

Conservation

PhyloP100: -0.360

Variant links:

Genes affected

ASPM (HGNC:19048): (assembly factor for spindle microtubules) This gene is the human ortholog of the Drosophila melanogaster 'abnormal spindle' gene (asp), which is essential for normal mitotic spindle function in embryonic neuroblasts. Studies in mouse also suggest a role of this gene in mitotic spindle regulation, with a preferential role in regulating neurogenesis. Mutations in this gene are associated with microcephaly primary type 5. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2011]

ASPM links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 1-197101577-G-A is Benign according to our data. Variant chr1-197101577-G-A is described in ClinVar as [Benign]. Clinvar id is 21604.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-197101577-G-A is described in Lovd as [Benign]. Variant chr1-197101577-G-A is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-0.36 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASPM	NM_018136.5 linkuse as main transcript	c.7674C>T	p.Ile2558=	synonymous_variant	18/28	ENST00000367409.9	NP_060606.3
ASPM	NM_001206846.2 linkuse as main transcript	c.4066-5413C>T		intron_variant			NP_001193775.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASPM	ENST00000367409.9 linkuse as main transcript	c.7674C>T	p.Ile2558=	synonymous_variant	18/28	1	NM_018136.5	ENSP00000356379	P1	Q8IZT6-1

Frequencies

GnomAD3 genomes

AF:

0.304

AC:

45981

AN:

151364

Hom.:

8702

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0941

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.399

Gnomad EAS

AF:

0.156

Gnomad SAS

AF:

0.290

Gnomad FIN

AF:

0.370

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.434

Gnomad OTH

AF:

0.333

GnomAD3 exomes

AF:

0.335

AC:

83114

AN:

248176

Hom.:

15547

AF XY:

0.346

AC XY:

46449

AN XY:

134320

show subpopulations

Gnomad AFR exome

AF:

0.0887

Gnomad AMR exome

AF:

0.210

Gnomad ASJ exome

AF:

0.390

Gnomad EAS exome

AF:

0.165

Gnomad SAS exome

AF:

0.307

Gnomad FIN exome

AF:

0.367

Gnomad NFE exome

AF:

0.431

Gnomad OTH exome

AF:

0.368

GnomAD4 exome

AF:

0.397

AC:

577479

AN:

1455666

Hom.:

120117

Cov.:

AF XY:

0.396

AC XY:

286790

AN XY:

724434

show subpopulations

Gnomad4 AFR exome

AF:

0.0823

Gnomad4 AMR exome

AF:

0.217

Gnomad4 ASJ exome

AF:

0.393

Gnomad4 EAS exome

AF:

0.154

Gnomad4 SAS exome

AF:

0.308

Gnomad4 FIN exome

AF:

0.371

Gnomad4 NFE exome

AF:

0.432

Gnomad4 OTH exome

AF:

0.371

GnomAD4 genome

AF:

0.304

AC:

45981

AN:

151482

Hom.:

8698

Cov.:

AF XY:

0.299

AC XY:

22132

AN XY:

73982

show subpopulations

Gnomad4 AFR

AF:

0.0939

Gnomad4 AMR

AF:

0.267

Gnomad4 ASJ

AF:

0.399

Gnomad4 EAS

AF:

0.157

Gnomad4 SAS

AF:

0.292

Gnomad4 FIN

AF:

0.370

Gnomad4 NFE

AF:

0.434

Gnomad4 OTH

AF:

0.331

Alfa

AF:

0.310

Hom.:

1460

Bravo

AF:

0.285

Asia WGS

AF:

0.201

AC:

702

AN:

3474

EpiCase

AF:

0.421

EpiControl

AF:

0.424

ClinVar

Significance: Benign

Submissions summary: Benign:11Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 18, 2013	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 08, 2013	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

Microcephaly 5, primary, autosomal recessive

Benign:3Other:1

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 14, 2021	- -

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Aug 02, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

4.2

DANN

Benign

0.66

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over