rs17110426

chr12-71921202-T-C

Variant summary

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

The NM_001146213.3(TBC1D15):c.1717-166T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0892 in 152,232 control chromosomes in the GnomAD database, including 685 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 (685 hom., cov: 33)
• Consequence: TBC1D15 NM_001146213.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

Genes affected

TBC1D15 (HGNC:25694): (TBC1 domain family member 15) This gene encodes a member of the Ras-like proteins in brain-GTPase activating protein superfamily that share a conserved Tre-2/Bub2/Cdc16 domain. The encoded protein interacts with Ras-like protein in brain 5A and may function as a regulator of intracellular trafficking. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBC1D15	NM_001146213.3	c.1717-166T>C		intron_variant		ENST00000485960.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBC1D15	ENST00000485960.7	c.1717-166T>C		intron_variant		1	NM_001146213.3	P3

Frequencies

GnomAD3 genomes AF: 0.0890 AC: 13545 AN: 152114 Hom.: 681 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0822

Gnomad ASJ AF: 0.0332

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0735

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0672

Gnomad OTH AF: 0.0812

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

GnomAD4 genome AF: 0.0892 AC: 13574 AN: 152232 Hom.: 685 Cov.: 33 AF XY: 0.0905 AC XY: 6733 AN XY: 74436

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0831

Gnomad4 ASJ AF: 0.0332

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0735

Gnomad4 NFE AF: 0.0671

Gnomad4 OTH AF: 0.0846

Alfa AF: 0.0557 Hom.: 147

Bravo AF: 0.0911

Asia WGS AF: 0.156 AC: 539 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	12
Dann	Benign	0.54

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: rs17110426; hg19: chr12-72314982;