rs1544285

Variant names:

• chr15-23019071-G-A
• rs1544285
• NM_052903.6:c.1487+148C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-23019071-G-A
• chr15-23019071-G-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.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
• Publications: 7 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=-0.88).
• BP6: Variant 15-23019071-G-A is Benign according to our data. Variant chr15-23019071-G-A is described in ClinVar as Benign. ClinVar VariationId 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 rank	MANE	Protein	UniProt
TUBGCP5	NM_052903.6	c.1487+148C>T		intron_variant	Intron 12 of 22	ENST00000615383.5	NP_443135.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUBGCP5	ENST00000615383.5	c.1487+148C>T		intron_variant	Intron 12 of 22	1	NM_052903.6	ENSP00000480316.1
TUBGCP5	ENST00000620435.4	c.1487+148C>T		intron_variant	Intron 12 of 21	2		ENSP00000481853.1
TUBGCP5	ENST00000614508.4	n.1487+148C>T		intron_variant	Intron 12 of 23	5		ENSP00000484566.1
TUBGCP5	ENST00000615455.1	n.1669+148C>T		intron_variant	Intron 3 of 5	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

African (AFR) AF: 0.912 AC: 9586 AN: 10510

American (AMR) AF: 0.518 AC: 6892 AN: 13308

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 7746 AN: 11698

East Asian (EAS) AF: 0.753 AC: 20800 AN: 27610

South Asian (SAS) AF: 0.660 AC: 14810 AN: 22428

European-Finnish (FIN) AF: 0.625 AC: 18993 AN: 30386

Middle Eastern (MID) AF: 0.627 AC: 1115 AN: 1778

European-Non Finnish (NFE) AF: 0.638 AC: 148372 AN: 232560

Other (OTH) AF: 0.657 AC: 14583 AN: 22190

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

African (AFR) AF: 0.919 AC: 38194 AN: 41548

American (AMR) AF: 0.578 AC: 8841 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2325 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3921 AN: 5176

South Asian (SAS) AF: 0.672 AC: 3245 AN: 4830

European-Finnish (FIN) AF: 0.642 AC: 6784 AN: 10574

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.640 AC: 43526 AN: 67976

Other (OTH) AF: 0.678 AC: 1434 AN: 2114

Alfa AF: 0.660 Hom.: 62333

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

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.77
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs1544285; hg19: chr15-22853997;