18-48992-A-G

Position:

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_001389610.1(TUBB8B):ā€‹c.149T>Cā€‹(p.Leu50Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Genomes: š‘“ 0.00042 ( 0 hom., cov: 31)
Exomes š‘“: 0.000027 ( 2 hom. )
Failed GnomAD Quality Control

Consequence

TUBB8B
NM_001389610.1 missense

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.65
Variant links:
Genes affected
TUBB8B (HGNC:24983): (tubulin beta 8B) Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization and mitotic cell cycle. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
Variant 18-48992-A-G is Benign according to our data. Variant chr18-48992-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2648508.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TUBB8BNM_001358689.2 linkc.225T>C p.Ser75Ser synonymous_variant 3/4 ENST00000308911.9 NP_001345618.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TUBB8BENST00000308911.9 linkc.225T>C p.Ser75Ser synonymous_variant 3/46 NM_001358689.2 ENSP00000496713.1 A6NNZ2
TUBB8BENST00000706408.1 linkn.1187T>C non_coding_transcript_exon_variant 4/5

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
60
AN:
146990
Hom.:
0
Cov.:
31
FAILED QC
Gnomad AFR
AF:
0.000826
Gnomad AMI
AF:
0.00233
Gnomad AMR
AF:
0.000746
Gnomad ASJ
AF:
0.000294
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000592
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000104
Gnomad OTH
AF:
0.000500
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000268
AC:
39
AN:
1454596
Hom.:
2
Cov.:
32
AF XY:
0.0000249
AC XY:
18
AN XY:
723796
show subpopulations
Gnomad4 AFR exome
AF:
0.000123
Gnomad4 AMR exome
AF:
0.000157
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000253
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000216
Gnomad4 OTH exome
AF:
0.0000334
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000422
AC:
62
AN:
147090
Hom.:
0
Cov.:
31
AF XY:
0.000488
AC XY:
35
AN XY:
71736
show subpopulations
Gnomad4 AFR
AF:
0.000875
Gnomad4 AMR
AF:
0.000745
Gnomad4 ASJ
AF:
0.000294
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000592
Gnomad4 NFE
AF:
0.000104
Gnomad4 OTH
AF:
0.000495
Alfa
AF:
0.000474
Hom.:
0

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 testingCeGaT Center for Human Genetics TuebingenJan 01, 2023TUBB8B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
6.4
DANN
Benign
0.44

Splicing

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: rs751460900; hg19: chr18-48992; API