13-112547538-ATGGGAAAGTCGCGCG-A

Position:

• chr13-112547538-ATGGGAAAGTCGCGCG-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4 BP6_Moderate BA1

The ENST00000464139.5(TUBGCP3):​c.1235_1249del​(p.Thr412_Pro416del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,240,746 control chromosomes in the GnomAD database, including 43,574 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.31 (5944 hom., cov: 0)
  • Exomes 𝑓: 0.20 (37630 hom.)
• Consequence: TUBGCP3 ENST00000464139.5 inframe_deletion
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.31

Genes affected

TUBGCP3 (HGNC:18598): (tubulin gamma complex component 3) Enables gamma-tubulin binding activity. Predicted to be involved in meiotic cell cycle; microtubule cytoskeleton organization; and mitotic cell cycle. Located in cytoplasm and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in ENST00000464139.5.
• BP6: Variant 13-112547538-ATGGGAAAGTCGCGCG-A is Benign according to our data. Variant chr13-112547538-ATGGGAAAGTCGCGCG-A is described in ClinVar as [Benign]. Clinvar id is 2672291.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBGCP3	NM_006322.6	c.1168+67_1168+81del		intron_variant		ENST00000261965.8	NP_006313.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUBGCP3	ENST00000261965.8	c.1168+67_1168+81del		intron_variant		1	NM_006322.6	ENSP00000261965	P1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 39065 AN: 127942 Hom.: 5935 Cov.: 0

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.299

GnomAD3 exomes AF: 0.206 AC: 24770 AN: 119980 Hom.: 3215 AF XY: 0.202 AC XY: 13148 AN XY: 65102

Gnomad AFR exome AF: 0.363

Gnomad AMR exome AF: 0.102

Gnomad ASJ exome AF: 0.174

Gnomad EAS exome AF: 0.327

Gnomad SAS exome AF: 0.156

Gnomad FIN exome AF: 0.154

Gnomad NFE exome AF: 0.210

Gnomad OTH exome AF: 0.181

GnomAD4 exome AF: 0.203 AC: 225334 AN: 1112712 Hom.: 37630 AF XY: 0.201 AC XY: 108536 AN XY: 539092

Gnomad4 AFR exome AF: 0.492

Gnomad4 AMR exome AF: 0.125

Gnomad4 ASJ exome AF: 0.201

Gnomad4 EAS exome AF: 0.441

Gnomad4 SAS exome AF: 0.146

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.193

Gnomad4 OTH exome AF: 0.215

GnomAD4 genome AF: 0.305 AC: 39108 AN: 128034 Hom.: 5944 Cov.: 0 AF XY: 0.297 AC XY: 18594 AN XY: 62562

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.303

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

research

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

Dec 12, 2023

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs142738218; hg19: chr13-113201852;