chr15-23000076-C-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052903.6. 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
	TUBGCP5	NM_052903.6	MANE Select	c.3029-210G>T		intron	N/A	NP_443135.3
	TUBGCP5	NM_001354372.2		c.3031+493G>T		intron	N/A	NP_001341301.1
	TUBGCP5	NM_001354373.2		c.3028+493G>T		intron	N/A	NP_001341302.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TUBGCP5	ENST00000615383.5	TSL:1 MANE Select	c.3029-210G>T		intron	N/A	ENSP00000480316.1	Q96RT8-1
	TUBGCP5	ENST00000959740.1		c.3005-210G>T		intron	N/A	ENSP00000629799.1
	TUBGCP5	ENST00000939427.1		c.2978-210G>T		intron	N/A	ENSP00000609486.1

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

African (AFR) AF: 0.574 AC: 23712 AN: 41330

American (AMR) AF: 0.346 AC: 5284 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1657 AN: 3464

East Asian (EAS) AF: 0.594 AC: 3045 AN: 5124

South Asian (SAS) AF: 0.499 AC: 2397 AN: 4806

European-Finnish (FIN) AF: 0.523 AC: 5517 AN: 10540

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.427 AC: 29023 AN: 67902

Other (OTH) AF: 0.448 AC: 949 AN: 2116

Alfa AF: 0.452 Hom.: 1961

Bravo AF: 0.466

Asia WGS AF: 0.547 AC: 1902 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.36
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs11631470; hg19: chr15-22872992;