NM_019020.4:c.*5032C>T

Variant names:

• chr17-79935827-G-A
• rs3743
• NM_019020.4:c.*5032C>T

Variant summary

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

The NM_019020.4(TBC1D16):​c.*5032C>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 0.297 in 152,048 control chromosomes in the GnomAD database, including 6,995 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 0.30 (6994 hom., cov: 32)
  • Exomes 𝑓: 0.30 (1 hom.)
• Consequence: TBC1D16 NM_019020.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 5 publications found

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]

LINC01978 (HGNC:52806): (long intergenic non-protein coding RNA 1978)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBC1D16	NM_019020.4	c.*5032C>T		3_prime_UTR_variant	Exon 12 of 12	ENST00000310924.7	NP_061893.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBC1D16	ENST00000310924.7	c.*5032C>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_019020.4	ENSP00000309794.2
TBC1D16	ENST00000576768.5	c.*5032C>T		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000461522.1
LINC01978	ENST00000771062.1	n.207-4472G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45196 AN: 151920 Hom.: 6982 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.305

GnomAD4 exome AF: 0.300 AC: 3 AN: 10 Hom.: 1 Cov.: 0 AF XY: 0.375 AC XY: 3 AN XY: 8

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.297 AC: 45226 AN: 152038 Hom.: 6994 Cov.: 32 AF XY: 0.302 AC XY: 22443 AN XY: 74312

African (AFR) AF: 0.224 AC: 9269 AN: 41456

American (AMR) AF: 0.369 AC: 5635 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3466

East Asian (EAS) AF: 0.417 AC: 2154 AN: 5166

South Asian (SAS) AF: 0.312 AC: 1507 AN: 4824

European-Finnish (FIN) AF: 0.324 AC: 3418 AN: 10552

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21695 AN: 67974

Other (OTH) AF: 0.301 AC: 634 AN: 2106

Alfa AF: 0.304 Hom.: 948

Bravo AF: 0.293

Asia WGS AF: 0.325 AC: 1131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.53
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3743; hg19: chr17-77909626;