chr15-23018631-T-C

Variant names:

• chr15-23018631-T-C
• rs748979
• NM_052903.6:c.1487+588A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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 -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 rank	MANE	Protein	UniProt
TUBGCP5	NM_052903.6	c.1487+588A>G		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+588A>G		intron_variant	Intron 12 of 22	1	NM_052903.6	ENSP00000480316.1
TUBGCP5	ENST00000620435.4	c.1487+588A>G		intron_variant	Intron 12 of 21	2		ENSP00000481853.1
TUBGCP5	ENST00000614508.4	n.1487+588A>G		intron_variant	Intron 12 of 23	5		ENSP00000484566.1
TUBGCP5	ENST00000615455.1	n.1669+588A>G		intron_variant	Intron 3 of 5	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

African (AFR) AF: 0.0422 AC: 1753 AN: 41564

American (AMR) AF: 0.0544 AC: 832 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3466

East Asian (EAS) AF: 0.457 AC: 2368 AN: 5178

South Asian (SAS) AF: 0.0827 AC: 399 AN: 4824

European-Finnish (FIN) AF: 0.0924 AC: 980 AN: 10604

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0958 AC: 6512 AN: 67998

Other (OTH) AF: 0.0766 AC: 162 AN: 2116

Alfa AF: 0.0849 Hom.: 111

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
PhyloP100		0.21

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: rs748979; hg19: chr15-22854437;