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GeneBe

1-197086652-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_018136.5(ASPM):c.10331+151A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 716,246 control chromosomes in the GnomAD database, including 278,520 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.78 ( 50021 hom., cov: 33)
Exomes 𝑓: 0.90 ( 228499 hom. )

Consequence

ASPM
NM_018136.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.659
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
Variant 1-197086652-T-C is Benign according to our data. Variant chr1-197086652-T-C is described in ClinVar as [Benign]. Clinvar id is 678055.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ASPMNM_018136.5 linkuse as main transcriptc.10331+151A>G intron_variant ENST00000367409.9
ASPMNM_001206846.2 linkuse as main transcriptc.5576+151A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ASPMENST00000367409.9 linkuse as main transcriptc.10331+151A>G intron_variant 1 NM_018136.5 P1Q8IZT6-1

Frequencies

GnomAD3 genomes
AF:
0.784
AC:
119227
AN:
152084
Hom.:
49998
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.451
Gnomad AMI
AF:
0.955
Gnomad AMR
AF:
0.871
Gnomad ASJ
AF:
0.902
Gnomad EAS
AF:
0.999
Gnomad SAS
AF:
0.898
Gnomad FIN
AF:
0.929
Gnomad MID
AF:
0.886
Gnomad NFE
AF:
0.910
Gnomad OTH
AF:
0.813
GnomAD4 exome
AF:
0.896
AC:
505323
AN:
564046
Hom.:
228499
AF XY:
0.898
AC XY:
271784
AN XY:
302768
show subpopulations
Gnomad4 AFR exome
AF:
0.442
Gnomad4 AMR exome
AF:
0.922
Gnomad4 ASJ exome
AF:
0.897
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
0.895
Gnomad4 FIN exome
AF:
0.931
Gnomad4 NFE exome
AF:
0.902
Gnomad4 OTH exome
AF:
0.879
GnomAD4 genome
AF:
0.784
AC:
119299
AN:
152200
Hom.:
50021
Cov.:
33
AF XY:
0.789
AC XY:
58687
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.451
Gnomad4 AMR
AF:
0.872
Gnomad4 ASJ
AF:
0.902
Gnomad4 EAS
AF:
0.999
Gnomad4 SAS
AF:
0.899
Gnomad4 FIN
AF:
0.929
Gnomad4 NFE
AF:
0.910
Gnomad4 OTH
AF:
0.815
Alfa
AF:
0.836
Hom.:
6870
Bravo
AF:
0.765
Asia WGS
AF:
0.918
AC:
3176
AN:
3460

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 19, 2018This 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. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
Cadd
Benign
1.7
Dann
Benign
0.45

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.

Other links and lift over

dbSNP: rs10733087; hg19: chr1-197055782; API