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GeneBe

1-197084463-GTTC-G

Variant summary

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

The NM_018136.5(ASPM):c.10332-40_10332-38del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00522 in 150550 control chromosomes in the gnomAD Genomes database, including 9 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0052 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 3 hom. )

Consequence

ASPM
NM_018136.5 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0310

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
?
Variant 1-197084463-GTTC-G is Benign according to our data. Variant chr1-197084463-GTTC-G is described in ClinVar as [Likely_benign]. Clinvar id is 1220309.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected. gnomad allele frequency = 0.00522 (786/150550) while in subpopulation AFR AF= 0.018 (738/41054). AF 95% confidence interval is 0.0169. There are 9 homozygotes in gnomad. There are 356 alleles in male gnomad subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 9 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ASPMNM_018136.5 linkuse as main transcriptc.10332-40_10332-38del intron_variant ENST00000367409.9
ASPMNM_001206846.2 linkuse as main transcriptc.5577-40_5577-38del intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ASPMENST00000367409.9 linkuse as main transcriptc.10332-40_10332-38del intron_variant 1 NM_018136.5 P1Q8IZT6-1

Frequencies

GnomAD3 genomes
AF:
0.00522
AC:
786
AN:
150550
Hom.:
9
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0180
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00266
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00323
Gnomad NFE
AF:
0.0000148
Gnomad OTH
AF:
0.00289
GnomAD3 exomes
AF:
0.00128
AC:
291
AN:
227884
Hom.:
3
AF XY:
0.00102
AC XY:
127
AN XY:
124398
show subpopulations
Gnomad AFR exome
AF:
0.0183
Gnomad AMR exome
AF:
0.000391
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000679
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000298
Gnomad OTH exome
AF:
0.000353
GnomAD4 exome
AF:
0.000535
AC:
686
AN:
1281836
Hom.:
7
AF XY:
0.000481
AC XY:
311
AN XY:
646094
show subpopulations
Gnomad4 AFR exome
AF:
0.0193
Gnomad4 AMR exome
AF:
0.000666
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000609
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000188
Gnomad4 OTH exome
AF:
0.00109
Alfa
AF:
0.00326
Hom.:
4
Bravo
AF:
0.00640

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 testingGeneDxMay 28, 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: rs537718986; hg19: chr1-197053593; API