chr6-30719937-T-A

Position:

• chr6-30719937-T-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000681435.1(TUBB):​c.-160+2298T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 151,964 control chromosomes in the GnomAD database, including 1,184 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.10 (1184 hom., cov: 32)
• Consequence: TUBB ENST00000681435.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.485

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 6-30719937-T-A is Benign according to our data. Variant chr6-30719937-T-A is described in ClinVar as [Benign]. Clinvar id is 1289698.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUBB	ENST00000681435.1	c.-160+2298T>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15251 AN: 151846 Hom.: 1179 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0797

Gnomad ASJ AF: 0.0843

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0469

Gnomad OTH AF: 0.107

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.100 AC: 15269 AN: 151964 Hom.: 1184 Cov.: 32 AF XY: 0.101 AC XY: 7503 AN XY: 74292

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.0795

Gnomad4 ASJ AF: 0.0843

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.0470

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0677 Hom.: 69

Bravo AF: 0.111

Asia WGS AF: 0.188 AC: 651 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 28, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.0
DANN	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9295910; hg19: chr6-30687714;