dbSNP rs1124736: TBC1D16:c.*1897G>T (chr17-79938962-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.369

Publications

6 publications found

Variant links:

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]

TBC1D16 links:

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

LINC01978 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TBC1D16	NM_019020.4 link	c.*1897G>T		3_prime_UTR_variant	Exon 12 of 12	ENST00000310924.7	NP_061893.2	Q8TBP0-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TBC1D16	ENST00000310924.7 link	c.*1897G>T	3_prime_UTR_variant	Exon 12 of 12	1	NM_019020.4	ENSP00000309794.2	Q8TBP0-1
TBC1D16	ENST00000340848.11 link	c.*1897G>T	3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000341517.7	Q8TBP0-2
TBC1D16	ENST00000576768.5 link	c.*1897G>T	3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000461522.1	Q8TBP0-4
LINC01978	ENST00000771062.1 link	n.207-1337C>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.373

AC:

56668

AN:

152062

Hom.:

10947

Cov.:

show subpopulations

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:

AN:

380

Hom.:

Cov.:

AF XY:

0.252

AC XY:

AN XY:

258

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.202

AC:

AN:

178

Middle Eastern (MID)

AF:

0.250

AC:

AN:

European-Non Finnish (NFE)

AF:

0.271

AC:

AN:

166

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.373

AC:

56727

AN:

152180

Hom.:

10975

Cov.:

AF XY:

0.363

AC XY:

27014

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.451

AC:

18713

AN:

41496

American (AMR)

AF:

0.290

AC:

4443

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.414

AC:

1437

AN:

3472

East Asian (EAS)

AF:

0.151

AC:

781

AN:

5176

South Asian (SAS)

AF:

0.253

AC:

1220

AN:

4824

European-Finnish (FIN)

AF:

0.341

AC:

3606

AN:

10590

Middle Eastern (MID)

AF:

0.449

AC:

132

AN:

294

European-Non Finnish (NFE)

AF:

0.371

AC:

25208

AN:

68004

Other (OTH)

AF:

0.370

AC:

782

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1883

3766

5650

7533

9416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

542

1084

1626

2168

2710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.369

Hom.:

24643

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

(source)

DANN

Benign

0.53

PhyloP100

0.37

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over