15-23003264-T-C

Variant names:

• chr15-23003264-T-C
• rs2251602
• NM_052903.6:c.2839-111A>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_052903.6(TUBGCP5):​c.2839-111A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 990,306 control chromosomes in the GnomAD database, including 49,055 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.29 (6933 hom., cov: 33)
  • Exomes 𝑓: 0.31 (42122 hom.)
• Consequence: TUBGCP5 NM_052903.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.226
• 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 15-23003264-T-C is Benign according to our data. Variant chr15-23003264-T-C is described in ClinVar as Benign. ClinVar VariationId is 1258455.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 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.2839-111A>G		intron	N/A	NP_443135.3
	TUBGCP5	NM_001354372.2		c.2842-111A>G		intron	N/A	NP_001341301.1
	TUBGCP5	NM_001354373.2		c.2839-111A>G		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.2839-111A>G		intron	N/A	ENSP00000480316.1	Q96RT8-1
	TUBGCP5	ENST00000620435.4	TSL:2	c.2839-111A>G		intron	N/A	ENSP00000481853.1	Q96RT8-2
	TUBGCP5	ENST00000959740.1		c.2815-111A>G		intron	N/A	ENSP00000629799.1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44311 AN: 151976 Hom.: 6932 Cov.: 33

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.294

GnomAD4 exome AF: 0.309 AC: 258808 AN: 838212 Hom.: 42122 AF XY: 0.312 AC XY: 134153 AN XY: 429412

African (AFR) AF: 0.239 AC: 5099 AN: 21368

American (AMR) AF: 0.198 AC: 6502 AN: 32900

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 6303 AN: 19236

East Asian (EAS) AF: 0.106 AC: 3614 AN: 34146

South Asian (SAS) AF: 0.360 AC: 22255 AN: 61810

European-Finnish (FIN) AF: 0.397 AC: 17569 AN: 44278

Middle Eastern (MID) AF: 0.260 AC: 1156 AN: 4450

European-Non Finnish (NFE) AF: 0.318 AC: 184485 AN: 580422

Other (OTH) AF: 0.299 AC: 11825 AN: 39602

GnomAD4 genome AF: 0.291 AC: 44325 AN: 152094 Hom.: 6933 Cov.: 33 AF XY: 0.294 AC XY: 21868 AN XY: 74324

African (AFR) AF: 0.240 AC: 9942 AN: 41494

American (AMR) AF: 0.243 AC: 3713 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3472

East Asian (EAS) AF: 0.0941 AC: 487 AN: 5174

South Asian (SAS) AF: 0.356 AC: 1714 AN: 4816

European-Finnish (FIN) AF: 0.410 AC: 4328 AN: 10556

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21969 AN: 67982

Other (OTH) AF: 0.294 AC: 621 AN: 2114

Alfa AF: 0.300 Hom.: 4285

Bravo AF: 0.274

Asia WGS AF: 0.261 AC: 906 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.38
DANN	Benign	0.65
PhyloP100		-0.23

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: rs2251602; hg19: chr15-22869804;