Menu
GeneBe

1-197084242-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong

The NM_018136.5(ASPM):c.*82G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000329 in 151910 control chromosomes in the gnomAD Genomes database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00033 ( 1 hom., cov: 32)

Consequence

ASPM
NM_018136.5 3_prime_UTR

Scores

2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.880

Links

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, gnomad allele frequency = 0.000329 (50/151910) while in subpopulation NFE AF= 0.0000883 (6/67964). AF 95% confidence interval is 0.0000376. There are 1 homozygotes in gnomad. There are 21 alleles in male gnomad subpopulation. Median coverage is 32. This position pass quality control queck.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ASPMNM_018136.5 linkuse as main transcriptc.*82G>A 3_prime_UTR_variant 28/28 ENST00000367409.9
ASPMNM_001206846.2 linkuse as main transcriptc.*82G>A 3_prime_UTR_variant 27/27

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ASPMENST00000367409.9 linkuse as main transcriptc.*82G>A 3_prime_UTR_variant 28/281 NM_018136.5 P1Q8IZT6-1
ASPMENST00000294732.11 linkuse as main transcriptc.*82G>A 3_prime_UTR_variant 27/271 Q8IZT6-2
ASPMENST00000367408.6 linkuse as main transcriptn.3803G>A non_coding_transcript_exon_variant 18/181
ASPMENST00000680265.1 linkuse as main transcriptc.*82G>A 3_prime_UTR_variant 29/29

Frequencies

GnomAD3 genomes
AF:
0.000329
AC:
50
AN:
151910
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.0127
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000883
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000436
AC:
377
AN:
865096
Hom.:
2
AF XY:
0.000425
AC XY:
192
AN XY:
451304
show subpopulations
Gnomad4 AFR exome
AF:
0.0000939
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0131
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000787
Gnomad4 OTH exome
AF:
0.00106
Alfa
AF:
0.000208
Hom.:
0
Bravo
AF:
0.000336

ClinVar

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

Submissions by phenotype

Microcephaly 5, primary, autosomal recessive Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
0.87
Dann
Benign
0.48
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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: rs775183015; hg19: chr1-197053372; API