15-73906472-T-G

Variant names:

• chr15-73906472-T-G
• rs4886467
• XM_011521281.4:c.979-3179T>G

Variant summary

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

The XM_011521281.4(TBC1D21):​c.979-3179T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,954 control chromosomes in the GnomAD database, including 29,041 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 0.61 (29041 hom., cov: 31)
• Consequence: TBC1D21 XM_011521281.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

TBC1D21 (HGNC:28536): (TBC1 domain family member 21) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Located in extracellular exosome. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBC1D21	XM_011521281.4	c.979-3179T>G		intron_variant	Intron 10 of 10		XP_011519583.1
TBC1D21	XM_011521283.3	c.979-770T>G		intron_variant	Intron 10 of 10		XP_011519585.1
TBC1D21	XM_047432198.1	c.871-3179T>G		intron_variant	Intron 9 of 9		XP_047288154.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93098 AN: 151836 Hom.: 29005 Cov.: 31

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.613 AC: 93187 AN: 151954 Hom.: 29041 Cov.: 31 AF XY: 0.617 AC XY: 45788 AN XY: 74270

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.612

Alfa AF: 0.576 Hom.: 43499

Bravo AF: 0.612

Asia WGS AF: 0.820 AC: 2849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.087
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4886467; hg19: chr15-74198813;