GeneBe

NM_018317.4:c.295-5849C>T

Variant names:

Variant summary

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

The NM_018317.4(TBC1D19):​c.295-5849C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,832 control chromosomes in the GnomAD database, including 11,781 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 0.38 ( 11781 hom., cov: 32)

Consequence

TBC1D19
NM_018317.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.57

Publications

1 publications found
Variant links:
Genes affected
TBC1D19 (HGNC:25624): (TBC1 domain family member 19) Predicted to enable GTPase activator activity. Predicted to be involved in regulation of catalytic activity. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TBC1D19NM_018317.4 linkc.295-5849C>T intron_variant Intron 4 of 20 ENST00000264866.9 NP_060787.2 Q8N5T2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TBC1D19ENST00000264866.9 linkc.295-5849C>T intron_variant Intron 4 of 20 1 NM_018317.4 ENSP00000264866.4 Q8N5T2-1

Frequencies

GnomAD3 genomes
AF:
0.377
AC:
57195
AN:
151714
Hom.:
11775
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.215
Gnomad AMI
AF:
0.575
Gnomad AMR
AF:
0.340
Gnomad ASJ
AF:
0.467
Gnomad EAS
AF:
0.352
Gnomad SAS
AF:
0.433
Gnomad FIN
AF:
0.422
Gnomad MID
AF:
0.437
Gnomad NFE
AF:
0.467
Gnomad OTH
AF:
0.394
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.377
AC:
57196
AN:
151832
Hom.:
11781
Cov.:
32
AF XY:
0.376
AC XY:
27869
AN XY:
74180
show subpopulations
African (AFR)
AF:
0.214
AC:
8880
AN:
41446
American (AMR)
AF:
0.339
AC:
5157
AN:
15198
Ashkenazi Jewish (ASJ)
AF:
0.467
AC:
1621
AN:
3468
East Asian (EAS)
AF:
0.351
AC:
1816
AN:
5174
South Asian (SAS)
AF:
0.432
AC:
2081
AN:
4818
European-Finnish (FIN)
AF:
0.422
AC:
4453
AN:
10544
Middle Eastern (MID)
AF:
0.446
AC:
131
AN:
294
European-Non Finnish (NFE)
AF:
0.467
AC:
31697
AN:
67876
Other (OTH)
AF:
0.398
AC:
837
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1744
3488
5232
6976
8720
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
554
1108
1662
2216
2770
<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:
0.430
Hom.:
2963
Bravo
AF:
0.364
Asia WGS
AF:
0.373
AC:
1296
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
7.0
DANN
Benign
0.41
PhyloP100
1.6
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: rs260960; hg19: chr4-26632984; API