rs8029844

Positions:

• chr15-73901131-C-T

Variant summary

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

The XM_011521281.4(TBC1D21):​c.979-8520C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.076 in 152,214 control chromosomes in the GnomAD database, including 920 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 0.076 (920 hom., cov: 32)
• Consequence: TBC1D21 XM_011521281.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.479

Genes affected

TBC1D21 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBC1D21	XM_011521281.4	c.979-8520C>T		intron_variant
TBC1D21	XM_011521283.3	c.979-6111C>T		intron_variant
TBC1D21	XM_047432198.1	c.871-8520C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0760 AC: 11564 AN: 152096 Hom.: 918 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0281

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0151

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0760 AC: 11574 AN: 152214 Hom.: 920 Cov.: 32 AF XY: 0.0784 AC XY: 5832 AN XY: 74416

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.0376

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0281

Gnomad4 NFE AF: 0.0151

Gnomad4 OTH AF: 0.0795

Alfa AF: 0.0274 Hom.: 354

Bravo AF: 0.0808

Asia WGS AF: 0.194 AC: 672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8029844; hg19: chr15-74193472;