rs748979

chr15-23018631-T-Cchr15-23018631-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052903.6(TUBGCP5):c.1487+588A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0888 in 152,248 control chromosomes in the GnomAD database, including 1,069 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.089 (1069 hom., cov: 32)
• Consequence: TUBGCP5 NM_052903.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUBGCP5	NM_052903.6	c.1487+588A>G		intron_variant		ENST00000615383.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUBGCP5	ENST00000615383.5	c.1487+588A>G		intron_variant		1	NM_052903.6	P1
TUBGCP5	ENST00000620435.4	c.1487+588A>G		intron_variant		2
TUBGCP5	ENST00000614508.4	c.1487+588A>G		intron_variant, NMD_transcript_variant		5
TUBGCP5	ENST00000615455.1	n.1669+588A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0888 AC: 13510 AN: 152130 Hom.: 1069 Cov.: 32

Gnomad AFR AF: 0.0422

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.0824

Gnomad FIN AF: 0.0924

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0888 AC: 13514 AN: 152248 Hom.: 1069 Cov.: 32 AF XY: 0.0902 AC XY: 6714 AN XY: 74436

Gnomad4 AFR AF: 0.0422

Gnomad4 AMR AF: 0.0544

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.0827

Gnomad4 FIN AF: 0.0924

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.0766

Alfa AF: 0.0865 Hom.: 110

Bravo AF: 0.0857

Asia WGS AF: 0.222 AC: 770 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	8.9
Dann	Benign	0.88

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

Publications

LitVar

Other links and lift over

dbSNP: rs748979; hg19: chr15-22854437;