6-30720290-C-G

Variant summary

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

The ENST00000681435.1(TUBB):​c.-159-2247C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0447 in 619,258 control chromosomes in the GnomAD database, including 1,432 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.080 ( 934 hom., cov: 32)
Exomes 𝑓: 0.033 ( 498 hom. )

Consequence

TUBB
ENST00000681435.1 intron

Scores

1
1

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.322
Variant links:
Genes affected
TUBB (HGNC:20778): (tubulin beta class I) This gene encodes a beta tubulin protein. This protein forms a dimer with alpha tubulin and acts as a structural component of microtubules. Mutations in this gene cause cortical dysplasia, complex, with other brain malformations 6. Alternative splicing results in multiple splice variants. There are multiple pseudogenes for this gene on chromosomes 1, 6, 7, 8, 9, and 13. [provided by RefSeq, Jun 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 6-30720290-C-G is Benign according to our data. Variant chr6-30720290-C-G is described in ClinVar as [Benign]. Clinvar id is 1233701.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TUBBENST00000681435.1 linkuse as main transcriptc.-159-2247C>G intron_variant ENSP00000506665

Frequencies

GnomAD3 genomes
AF:
0.0794
AC:
12083
AN:
152100
Hom.:
930
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.199
Gnomad AMI
AF:
0.00329
Gnomad AMR
AF:
0.0645
Gnomad ASJ
AF:
0.0626
Gnomad EAS
AF:
0.00212
Gnomad SAS
AF:
0.00704
Gnomad FIN
AF:
0.0153
Gnomad MID
AF:
0.0728
Gnomad NFE
AF:
0.0326
Gnomad OTH
AF:
0.0918
GnomAD4 exome
AF:
0.0334
AC:
15593
AN:
467040
Hom.:
498
Cov.:
4
AF XY:
0.0313
AC XY:
7771
AN XY:
248184
show subpopulations
Gnomad4 AFR exome
AF:
0.201
Gnomad4 AMR exome
AF:
0.0538
Gnomad4 ASJ exome
AF:
0.0631
Gnomad4 EAS exome
AF:
0.00129
Gnomad4 SAS exome
AF:
0.00752
Gnomad4 FIN exome
AF:
0.0151
Gnomad4 NFE exome
AF:
0.0321
Gnomad4 OTH exome
AF:
0.0448
GnomAD4 genome
AF:
0.0796
AC:
12110
AN:
152218
Hom.:
934
Cov.:
32
AF XY:
0.0757
AC XY:
5634
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.199
Gnomad4 AMR
AF:
0.0644
Gnomad4 ASJ
AF:
0.0626
Gnomad4 EAS
AF:
0.00212
Gnomad4 SAS
AF:
0.00705
Gnomad4 FIN
AF:
0.0153
Gnomad4 NFE
AF:
0.0326
Gnomad4 OTH
AF:
0.0908
Alfa
AF:
0.0186
Hom.:
24
Bravo
AF:
0.0878
Asia WGS
AF:
0.0240
AC:
84
AN:
3478

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 30, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
12
DANN
Uncertain
0.98

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: rs17189357; hg19: chr6-30688067; API