12-49129740-GAT-G

Position:

• chr12-49129740-GAT-G

Variant summary

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

The NM_006082.3(TUBA1B):​c.4-20_4-19del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 1,612,602 control chromosomes in the GnomAD database, including 98,766 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.28 (7439 hom., cov: 22)
  • Exomes 𝑓: 0.34 (91327 hom.)
• Consequence: TUBA1B NM_006082.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.21

Genes affected

TUBA1B (HGNC:18809): (tubulin alpha 1b) Enables double-stranded RNA binding activity and ubiquitin protein ligase binding activity. Predicted to be involved in microtubule cytoskeleton organization and mitotic cell cycle. Predicted to act upstream of or within cellular response to interleukin-4. Located in microtubule. [provided by Alliance of Genome Resources, Apr 2022]

TUBA1B-AS1 (HGNC:56356): (TUBA1B antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 12-49129740-GAT-G is Benign according to our data. Variant chr12-49129740-GAT-G is described in ClinVar as [Benign]. Clinvar id is 1264540.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUBA1B	NM_006082.3	c.4-20_4-19del		intron_variant		ENST00000336023.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUBA1B	ENST00000336023.9	c.4-20_4-19del		intron_variant		1	NM_006082.3	P1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42884 AN: 151818 Hom.: 7438 Cov.: 22

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.278

GnomAD3 exomes AF: 0.358 AC: 89759 AN: 250540 Hom.: 18417 AF XY: 0.367 AC XY: 49794 AN XY: 135496

Gnomad AFR exome AF: 0.101

Gnomad AMR exome AF: 0.312

Gnomad ASJ exome AF: 0.236

Gnomad EAS exome AF: 0.729

Gnomad SAS exome AF: 0.474

Gnomad FIN exome AF: 0.403

Gnomad NFE exome AF: 0.321

Gnomad OTH exome AF: 0.340

GnomAD4 exome AF: 0.343 AC: 500647 AN: 1460666 Hom.: 91327 AF XY: 0.346 AC XY: 251740 AN XY: 726640

Gnomad4 AFR exome AF: 0.0972

Gnomad4 AMR exome AF: 0.308

Gnomad4 ASJ exome AF: 0.242

Gnomad4 EAS exome AF: 0.708

Gnomad4 SAS exome AF: 0.470

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.329

Gnomad4 OTH exome AF: 0.339

GnomAD4 genome AF: 0.282 AC: 42891 AN: 151936 Hom.: 7439 Cov.: 22 AF XY: 0.291 AC XY: 21613 AN XY: 74218

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.276

Alfa AF: 0.295 Hom.: 865

Bravo AF: 0.265

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

Apr 19, 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: rs34070757; hg19: chr12-49523523;