rs6582065

Variant summary

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

The NM_001146213.3(TBC1D15):​c.1183+1445T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,196 control chromosomes in the GnomAD database, including 3,635 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 0.18 ( 3635 hom., cov: 32)

Consequence

TBC1D15
NM_001146213.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.306

Publications

5 publications found
Variant links:
Genes affected
TBC1D15 (HGNC:25694): (TBC1 domain family member 15) This gene encodes a member of the Ras-like proteins in brain-GTPase activating protein superfamily that share a conserved Tre-2/Bub2/Cdc16 domain. The encoded protein interacts with Ras-like protein in brain 5A and may function as a regulator of intracellular trafficking. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

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=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TBC1D15NM_001146213.3 linkc.1183+1445T>C intron_variant Intron 10 of 16 ENST00000485960.7 NP_001139685.2 Q8TC07-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TBC1D15ENST00000485960.7 linkc.1183+1445T>C intron_variant Intron 10 of 16 1 NM_001146213.3 ENSP00000420678.2 Q8TC07-2

Frequencies

GnomAD3 genomes
AF:
0.175
AC:
26644
AN:
152078
Hom.:
3621
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.385
Gnomad AMI
AF:
0.0724
Gnomad AMR
AF:
0.102
Gnomad ASJ
AF:
0.106
Gnomad EAS
AF:
0.0417
Gnomad SAS
AF:
0.151
Gnomad FIN
AF:
0.0815
Gnomad MID
AF:
0.0791
Gnomad NFE
AF:
0.0971
Gnomad OTH
AF:
0.149
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.175
AC:
26697
AN:
152196
Hom.:
3635
Cov.:
32
AF XY:
0.173
AC XY:
12873
AN XY:
74434
show subpopulations
African (AFR)
AF:
0.385
AC:
15958
AN:
41478
American (AMR)
AF:
0.101
AC:
1551
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.106
AC:
368
AN:
3466
East Asian (EAS)
AF:
0.0418
AC:
217
AN:
5186
South Asian (SAS)
AF:
0.150
AC:
724
AN:
4824
European-Finnish (FIN)
AF:
0.0815
AC:
865
AN:
10618
Middle Eastern (MID)
AF:
0.0850
AC:
25
AN:
294
European-Non Finnish (NFE)
AF:
0.0971
AC:
6601
AN:
68016
Other (OTH)
AF:
0.153
AC:
322
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
980
1960
2941
3921
4901
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
276
552
828
1104
1380
<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:
0.111
Hom.:
2165
Bravo
AF:
0.183
Asia WGS
AF:
0.133
AC:
463
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.8
DANN
Benign
0.37
PhyloP100
-0.31
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

Publications

Other links and lift over

dbSNP: rs6582065; hg19: chr12-72293166; API