chr15-23000076-C-A

Variant names:

• chr15-23000076-C-A
• rs11631470
• NM_052903.6:c.3029-210G>T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_052903.6(TUBGCP5):​c.3029-210G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,736 control chromosomes in the GnomAD database, including 17,712 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (17712 hom., cov: 32)
• Consequence: TUBGCP5 NM_052903.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0150

Genes affected

TUBGCP5 (HGNC:18600): (tubulin gamma complex component 5) Enables microtubule binding activity. Involved in microtubule nucleation. Located in centrosome and cytosol. Part of gamma-tubulin large complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 15-23000076-C-A is Benign according to our data. Variant chr15-23000076-C-A is described in ClinVar as [Benign]. Clinvar id is 1288443.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUBGCP5	NM_052903.6	c.3029-210G>T		intron_variant	Intron 22 of 22	ENST00000615383.5	NP_443135.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUBGCP5	ENST00000615383.5	c.3029-210G>T		intron_variant	Intron 22 of 22	1	NM_052903.6	ENSP00000480316.1
TUBGCP5	ENST00000614508.4	n.3028+493G>T		intron_variant	Intron 22 of 23	5		ENSP00000484566.1
TUBGCP5	ENST00000620435.4	c.*446G>T		downstream_gene_variant		2		ENSP00000481853.1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72002 AN: 151618 Hom.: 17679 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.475 AC: 72085 AN: 151736 Hom.: 17712 Cov.: 32 AF XY: 0.478 AC XY: 35449 AN XY: 74108

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.448

Alfa AF: 0.452 Hom.: 1961

Bravo AF: 0.466

Asia WGS AF: 0.547 AC: 1902 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11631470; hg19: chr15-22872992;