6-3224590-GA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_178012.5(TUBB2B):c.*160del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.94 (66879 hom., cov: 0)
  • Exomes 𝑓: 0.94 (399385 hom.)
• Consequence: TUBB2B NM_178012.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.235

Genes affected

TUBB2B (HGNC:30829): (tubulin beta 2B class IIb) The protein encoded by this gene is a beta isoform of tubulin, which binds GTP and is a major component of microtubules. This gene is highly similar to TUBB2A and TUBB2C. Defects in this gene are a cause of asymmetric polymicrogyria. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-3224590-GA-G is Benign according to our data. Variant chr6-3224590-GA-G is described in ClinVar as [Benign]. Clinvar id is 1261368.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUBB2B	NM_178012.5	c.*160del		3_prime_UTR_variant	4/4	ENST00000259818.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUBB2B	ENST00000259818.8	c.*160del		3_prime_UTR_variant	4/4	1	NM_178012.5	P1

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142285 AN: 151978 Hom.: 66829 Cov.: 0

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.917

GnomAD4 exome AF: 0.935 AC: 851594 AN: 910380 Hom.: 399385 Cov.: 0 AF XY: 0.934 AC XY: 423418 AN XY: 453546

Gnomad4 AFR exome AF: 0.961

Gnomad4 AMR exome AF: 0.862

Gnomad4 ASJ exome AF: 0.875

Gnomad4 EAS exome AF: 0.764

Gnomad4 SAS exome AF: 0.877

Gnomad4 FIN exome AF: 0.972

Gnomad4 NFE exome AF: 0.950

Gnomad4 OTH exome AF: 0.926

GnomAD4 genome AF: 0.936 AC: 142394 AN: 152096 Hom.: 66879 Cov.: 0 AF XY: 0.934 AC XY: 69464 AN XY: 74346

Gnomad4 AFR AF: 0.959

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.974

Gnomad4 NFE AF: 0.951

Gnomad4 OTH AF: 0.916

Bravo AF: 0.928

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

Aug 05, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs10717744; hg19: chr6-3224824;