rs1544285

Positions:

• chr15-23019071-G-A
• chr15-23019071-G-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.1487+148C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 524,640 control chromosomes in the GnomAD database, including 120,788 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.72 (40428 hom., cov: 34)
  • Exomes 𝑓: 0.65 (80360 hom.)
• Consequence: TUBGCP5 NM_052903.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.108

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]

TUBGCP5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 15-23019071-G-A is Benign according to our data. Variant chr15-23019071-G-A is described in ClinVar as [Benign]. Clinvar id is 1245202.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBGCP5	NM_052903.6	c.1487+148C>T		intron_variant		ENST00000615383.5	NP_443135.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUBGCP5	ENST00000615383.5	c.1487+148C>T		intron_variant		1	NM_052903.6	ENSP00000480316.1
TUBGCP5	ENST00000620435.4	c.1487+148C>T		intron_variant		2		ENSP00000481853.1
TUBGCP5	ENST00000614508.4	n.1487+148C>T		intron_variant		5		ENSP00000484566.1
TUBGCP5	ENST00000615455.1	n.1669+148C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108939 AN: 152054 Hom.: 40377 Cov.: 34

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.682

GnomAD4 exome AF: 0.652 AC: 242897 AN: 372468 Hom.: 80360 AF XY: 0.653 AC XY: 125233 AN XY: 191824

Gnomad4 AFR exome AF: 0.912

Gnomad4 AMR exome AF: 0.518

Gnomad4 ASJ exome AF: 0.662

Gnomad4 EAS exome AF: 0.753

Gnomad4 SAS exome AF: 0.660

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.638

Gnomad4 OTH exome AF: 0.657

GnomAD4 genome AF: 0.717 AC: 109040 AN: 152172 Hom.: 40428 Cov.: 34 AF XY: 0.714 AC XY: 53109 AN XY: 74378

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.678

Alfa AF: 0.654 Hom.: 44190

Bravo AF: 0.715

Asia WGS AF: 0.714 AC: 2484 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1544285; hg19: chr15-22853997;