3-17832158-G-A

Variant names:

• chr3-17832158-G-A
• rs2337387
• ENST00000414318.2:n.212-524024C>T

Variant summary

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

The ENST00000414318.2(TBC1D5):​n.212-524024C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,892 control chromosomes in the GnomAD database, including 21,534 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 0.52 (21534 hom., cov: 31)
• Consequence: TBC1D5 ENST00000414318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 3 publications found

Genes affected

TBC1D5 (HGNC:19166): (TBC1 domain family member 5) Enables AP-2 adaptor complex binding activity and retromer complex binding activity. Involved in several processes, including macroautophagy; positive regulation of receptor internalization; and retrograde transport, endosome to Golgi. Located in Golgi apparatus; autophagosome; and endosome membrane. Part of retromer complex. Colocalizes with AP-2 adaptor complex and Atg1/ULK1 kinase 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBC1D5	ENST00000414318.2	n.212-524024C>T		intron_variant	Intron 1 of 8	5

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79132 AN: 151776 Hom.: 21510 Cov.: 31

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.521 AC: 79208 AN: 151892 Hom.: 21534 Cov.: 31 AF XY: 0.530 AC XY: 39363 AN XY: 74224

African (AFR) AF: 0.502 AC: 20788 AN: 41418

American (AMR) AF: 0.580 AC: 8840 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1762 AN: 3464

East Asian (EAS) AF: 0.979 AC: 5067 AN: 5176

South Asian (SAS) AF: 0.617 AC: 2965 AN: 4804

European-Finnish (FIN) AF: 0.564 AC: 5931 AN: 10518

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32221 AN: 67956

Other (OTH) AF: 0.505 AC: 1062 AN: 2104

Alfa AF: 0.505 Hom.: 4206

Bravo AF: 0.521

Asia WGS AF: 0.770 AC: 2673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.69
DANN	Benign	0.13
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2337387; hg19: chr3-17873650;