Menu
GeneBe

1-197084431-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_018136.5(ASPM):c.10332-6del 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 Likely benign (★).

Frequency

Genomes: 𝑓 0.0035 ( 2 hom., cov: 0)

Consequence

ASPM
NM_018136.5 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.439

Links

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
?
Variant 1-197084431-TA-T is Benign according to our data. Variant chr1-197084431-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 1204775.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-197084431-TA-T is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected. gnomad allele frequency = 0.0035 (500/143052) while in subpopulation AFR AF= 0.00477 (184/38598). AF 95% confidence interval is 0.0042. There are 2 homozygotes in gnomad. There are 270 alleles in male gnomad subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ASPMNM_018136.5 linkuse as main transcriptc.10332-6del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000367409.9
ASPMNM_001206846.2 linkuse as main transcriptc.5577-6del 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.10332-6del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_018136.5 P1Q8IZT6-1

Frequencies

GnomAD3 genomes
AF:
0.00350
AC:
500
AN:
143052
Hom.:
2
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00477
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00343
Gnomad ASJ
AF:
0.00149
Gnomad EAS
AF:
0.00142
Gnomad SAS
AF:
0.000885
Gnomad FIN
AF:
0.0149
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00180
Gnomad OTH
AF:
0.00155
GnomAD4 exome
AF:
0.133
AC:
157885
AN:
1186624
Hom.:
1
AF XY:
0.135
AC XY:
80485
AN XY:
594382
show subpopulations
Gnomad4 AFR exome
AF:
0.241
Gnomad4 AMR exome
AF:
0.252
Gnomad4 ASJ exome
AF:
0.142
Gnomad4 EAS exome
AF:
0.261
Gnomad4 SAS exome
AF:
0.189
Gnomad4 FIN exome
AF:
0.149
Gnomad4 NFE exome
AF:
0.115
Gnomad4 OTH exome
AF:
0.143

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely 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)
0.010
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