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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019020.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TBC1D16	NM_019020.4	MANE Select	c.*1897G>T	3_prime_UTR	Exon 12 of 12	NP_061893.2
TBC1D16	NM_001271845.2		c.*1897G>T	3_prime_UTR	Exon 8 of 8	NP_001258774.1	Q8TBP0-2
TBC1D16	NM_001271844.2		c.*1897G>T	3_prime_UTR	Exon 8 of 8	NP_001258773.1	Q8TBP0-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TBC1D16	ENST00000310924.7	TSL:1 MANE Select	c.*1897G>T	3_prime_UTR	Exon 12 of 12	ENSP00000309794.2	Q8TBP0-1
TBC1D16	ENST00000340848.11	TSL:1	c.*1897G>T	3_prime_UTR	Exon 8 of 8	ENSP00000341517.7	Q8TBP0-2
TBC1D16	ENST00000576768.5	TSL:1	c.*1897G>T	3_prime_UTR	Exon 8 of 8	ENSP00000461522.1	Q8TBP0-4

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over