chr15-22996179-G-A

Variant names:

• chr15-22996179-G-A
• rs765763
• NM_001354372.2:c.3031+4390C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001354372.2(TUBGCP5):​c.3031+4390C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,138 control chromosomes in the GnomAD database, including 9,786 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 0.35 (9786 hom., cov: 33)
• Consequence: TUBGCP5 NM_001354372.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 6 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=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUBGCP5	NM_001354372.2	c.3031+4390C>T		intron_variant	Intron 22 of 22		NP_001341301.1
TUBGCP5	NM_001354373.2	c.3028+4390C>T		intron_variant	Intron 22 of 22		NP_001341302.1
TUBGCP5	NM_001354374.2	c.2986+4390C>T		intron_variant	Intron 22 of 22		NP_001341303.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUBGCP5	ENST00000614508.4	n.*61+666C>T		intron_variant	Intron 23 of 23	5		ENSP00000484566.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52765 AN: 152020 Hom.: 9777 Cov.: 33

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.0942

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.347 AC: 52796 AN: 152138 Hom.: 9786 Cov.: 33 AF XY: 0.347 AC XY: 25839 AN XY: 74382

African (AFR) AF: 0.434 AC: 18027 AN: 41494

American (AMR) AF: 0.260 AC: 3981 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1185 AN: 3470

East Asian (EAS) AF: 0.0941 AC: 488 AN: 5188

South Asian (SAS) AF: 0.356 AC: 1718 AN: 4824

European-Finnish (FIN) AF: 0.410 AC: 4334 AN: 10576

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21989 AN: 67986

Other (OTH) AF: 0.333 AC: 704 AN: 2114

Alfa AF: 0.328 Hom.: 25684

Bravo AF: 0.336

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	5.7
DANN	Benign	0.93
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs765763; hg19: chr15-22876889;