2-219253950-CGG-C

Variant names:

• chr2-219253950-CGG-C
• rs3051654
• NM_001355221.1:c.12+540_12+541delGG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001355221.1(TUBA4B):​c.12+540_12+541delGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000055 in 509,124 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000032 (0 hom., cov: 30)
  • Exomes 𝑓: 0.000063 (0 hom.)
• Consequence: TUBA4B NM_001355221.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 0 publications found

Genes affected

TUBA4B (HGNC:18637): (tubulin alpha 4b) 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. Predicted to be active in cytoplasm and microtubule. [provided by Alliance of Genome Resources, Apr 2022]

TUBA4A (HGNC:12407): (tubulin alpha 4a) Microtubules of the eukaryotic cytoskeleton perform essential and diverse functions and are composed of a heterodimer of alpha and beta tubulin. The genes encoding these microtubule constituents are part of the tubulin superfamily, which is composed of six distinct families. Genes from the alpha, beta and gamma tubulin families are found in all eukaryotes. The alpha and beta tubulins represent the major components of microtubules, while gamma tubulin plays a critical role in the nucleation of microtubule assembly. There are multiple alpha and beta tubulin genes and they are highly conserved among and between species. This gene encodes an alpha tubulin that is a highly conserved homolog of a rat testis-specific alpha tubulin. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2013]

TUBA4A Gene-Disease associations (from GenCC):

• amyotrophic lateral sclerosis type 22

  Inheritance: AD, Unknown Classification: MODERATE, LIMITED Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen
• autosomal dominant macrothrombocytopenia

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001355221.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TUBA4B	NM_001355221.1	MANE Select	c.12+540_12+541delGG		intron	N/A	NP_001342150.1	Q9H853
	TUBA4A	NM_001278552.2		c.-43+143_-43+144delCC		intron	N/A	NP_001265481.1	P68366-2
	TUBA4A	NM_006000.3	MANE Select	c.-94_-93delCC		upstream_gene	N/A	NP_005991.1	P68366-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TUBA4B	ENST00000490341.3	TSL:2 MANE Select	c.12+532_12+533delGG		intron	N/A	ENSP00000487719.1	Q9H853
	TUBA4B	ENST00000473885.5	TSL:1	n.177+532_177+533delGG		intron	N/A
	TUBA4B	ENST00000485041.5	TSL:1	n.177+532_177+533delGG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000317 AC: 4 AN: 126366 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.0000276

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000717

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000627 AC: 24 AN: 382698 Hom.: 0 AF XY: 0.0000643 AC XY: 12 AN XY: 186650

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000170 AC: 2 AN: 11774

American (AMR) AF: 0.00 AC: 0 AN: 5396

Ashkenazi Jewish (ASJ) AF: 0.000134 AC: 1 AN: 7446

East Asian (EAS) AF: 0.000113 AC: 2 AN: 17650

South Asian (SAS) AF: 0.000315 AC: 3 AN: 9512

European-Finnish (FIN) AF: 0.0000425 AC: 1 AN: 23510

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1324

European-Non Finnish (NFE) AF: 0.0000416 AC: 12 AN: 288192

Other (OTH) AF: 0.000168 AC: 3 AN: 17894

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00176073), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0000316 AC: 4 AN: 126426 Hom.: 0 Cov.: 30 AF XY: 0.0000163 AC XY: 1 AN XY: 61470

African (AFR) AF: 0.0000276 AC: 1 AN: 36272

American (AMR) AF: 0.00 AC: 0 AN: 12740

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2904

East Asian (EAS) AF: 0.000720 AC: 3 AN: 4166

South Asian (SAS) AF: 0.00 AC: 0 AN: 3696

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8134

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 220

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 55828

Other (OTH) AF: 0.00 AC: 0 AN: 1718

Alfa AF: 0.00 Hom.: 7

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.43

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

Other links and lift over

dbSNP: rs3051654; hg19: chr2-220118672;