rs1124736

chr17-79938962-C-A

Variant summary

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

The NM_019020.4(TBC1D16):c.*1897G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,560 control chromosomes in the GnomAD database, including 10,982 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 0.37 (10975 hom., cov: 33)
  • Exomes 𝑓: 0.25 (7 hom.)
• Consequence: TBC1D16 NM_019020.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369

Genes affected

TBC1D16 (HGNC:28356): (TBC1 domain family member 16) Enables GTPase activator activity. Involved in regulation of receptor recycling. Located in cytosol and early endosome. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBC1D16	NM_019020.4	c.*1897G>T		3_prime_UTR_variant	12/12	ENST00000310924.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBC1D16	ENST00000310924.7	c.*1897G>T		3_prime_UTR_variant	12/12	1	NM_019020.4	P1
TBC1D16	ENST00000340848.11	c.*1897G>T		3_prime_UTR_variant	8/8	1
TBC1D16	ENST00000576768.5	c.*1897G>T		3_prime_UTR_variant	8/8	1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56668 AN: 152062 Hom.: 10947 Cov.: 33

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.367

GnomAD4 exome AF: 0.247 AC: 94 AN: 380 Hom.: 7 Cov.: 0 AF XY: 0.252 AC XY: 65 AN XY: 258

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.271

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.373 AC: 56727 AN: 152180 Hom.: 10975 Cov.: 33 AF XY: 0.363 AC XY: 27014 AN XY: 74392

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.370

Alfa AF: 0.369 Hom.: 15203

Bravo AF: 0.375

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.3
Dann	Benign	0.53

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: rs1124736; hg19: chr17-77912761;