13-112570253-A-G

Variant names:

• chr13-112570253-A-G
• rs9324313
• NM_006322.6:c.77-994T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006322.6(TUBGCP3):​c.77-994T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 152,074 control chromosomes in the GnomAD database, including 19,765 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (19765 hom., cov: 32)
• Consequence: TUBGCP3 NM_006322.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUBGCP3	NM_006322.6	c.77-994T>C		intron_variant	Intron 1 of 21	ENST00000261965.8	NP_006313.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUBGCP3	ENST00000261965.8	c.77-994T>C		intron_variant	Intron 1 of 21	1	NM_006322.6	ENSP00000261965.3

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68238 AN: 151956 Hom.: 19712 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.449 AC: 68348 AN: 152074 Hom.: 19765 Cov.: 32 AF XY: 0.439 AC XY: 32654 AN XY: 74326

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.439

Alfa AF: 0.290 Hom.: 1473

Bravo AF: 0.475

Asia WGS AF: 0.409 AC: 1425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.51

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: rs9324313; hg19: chr13-113224567;