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1-197084431-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_018136.5(ASPM):c.10332-6_10332-5insT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.33 ( 8683 hom., cov: 0)

Consequence

ASPM
NM_018136.5 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.439

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
?
Variant 1-197084431-T-TA is Benign according to our data. Variant chr1-197084431-T-TA is described in ClinVar as [Benign]. Clinvar id is 1238332.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ASPMNM_018136.5 linkuse as main transcriptc.10332-6_10332-5insT splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000367409.9
ASPMNM_001206846.2 linkuse as main transcriptc.5577-6_5577-5insT splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ASPMENST00000367409.9 linkuse as main transcriptc.10332-6_10332-5insT splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_018136.5 P1Q8IZT6-1

Frequencies

GnomAD3 genomes
AF:
0.334
AC:
47758
AN:
143130
Hom.:
8683
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.174
Gnomad AMI
AF:
0.413
Gnomad AMR
AF:
0.287
Gnomad ASJ
AF:
0.418
Gnomad EAS
AF:
0.179
Gnomad SAS
AF:
0.295
Gnomad FIN
AF:
0.371
Gnomad MID
AF:
0.468
Gnomad NFE
AF:
0.440
Gnomad OTH
AF:
0.348

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 testingGeneDxAug 10, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs200839523; hg19: chr1-197053561; API