22-18110474-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000474897.6(ENSG00000288683):n.815-11005C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00179 in 320,988 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0035 ( 4 hom., cov: 32)
Exomes 𝑓: 0.00021 ( 1 hom. )
Consequence
ENSG00000288683
ENST00000474897.6 intron
ENST00000474897.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.35
Genes affected
TUBA8 (HGNC:12410): (tubulin alpha 8) This gene encodes a member of the alpha tubulin protein family. Alpha tubulins are one of two core protein families (alpha and beta tubulins) that heterodimerize and assemble to form microtubules. Mutations in this gene are associated with polymicrogyria and optic nerve hypoplasia. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 22-18110474-C-T is Benign according to our data. Variant chr22-18110474-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1199579.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 4 gene
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 |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000288683 | ENST00000474897.6 | n.815-11005C>T | intron_variant | 5 | ENSP00000434235.2 | |||||
TUBA8 | ENST00000680175.1 | c.-392C>T | 5_prime_UTR_variant | 1/6 | ENSP00000505461.1 | |||||
TUBA8 | ENST00000679963.1 | c.-298C>T | 5_prime_UTR_variant | 1/5 | ENSP00000505896.1 | |||||
TUBA8 | ENST00000426208.5 | c.-298C>T | 5_prime_UTR_variant | 1/3 | 3 | ENSP00000407624.1 |
Frequencies
GnomAD3 genomes AF: 0.00354 AC: 539AN: 152220Hom.: 4 Cov.: 32
GnomAD3 genomes
AF:
AC:
539
AN:
152220
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.000213 AC: 36AN: 168650Hom.: 1 Cov.: 0 AF XY: 0.000167 AC XY: 15AN XY: 89876
GnomAD4 exome
AF:
AC:
36
AN:
168650
Hom.:
Cov.:
0
AF XY:
AC XY:
15
AN XY:
89876
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00354 AC: 539AN: 152338Hom.: 4 Cov.: 32 AF XY: 0.00337 AC XY: 251AN XY: 74500
GnomAD4 genome
AF:
AC:
539
AN:
152338
Hom.:
Cov.:
32
AF XY:
AC XY:
251
AN XY:
74500
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
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 submitter | clinical testing | GeneDx | Dec 24, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at