GeneBe

NM_145647.4:c.2641-227C>T

Variant names:

Variant summary

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

The NM_145647.4(TBC1D31):​c.2641-227C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,320 control chromosomes in the GnomAD database, including 10,047 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 0.34 ( 10047 hom., cov: 28)

Consequence

TBC1D31
NM_145647.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

3 publications found
Variant links:
Genes affected
TBC1D31 (HGNC:30888): (TBC1 domain family member 31) Located in centrosome. [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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TBC1D31NM_145647.4 linkc.2641-227C>T intron_variant Intron 18 of 21 ENST00000287380.6 NP_663622.2 Q96DN5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TBC1D31ENST00000287380.6 linkc.2641-227C>T intron_variant Intron 18 of 21 1 NM_145647.4 ENSP00000287380.1 Q96DN5-1

Frequencies

GnomAD3 genomes
AF:
0.344
AC:
52009
AN:
151202
Hom.:
10019
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.525
Gnomad AMI
AF:
0.167
Gnomad AMR
AF:
0.273
Gnomad ASJ
AF:
0.264
Gnomad EAS
AF:
0.203
Gnomad SAS
AF:
0.230
Gnomad FIN
AF:
0.299
Gnomad MID
AF:
0.228
Gnomad NFE
AF:
0.284
Gnomad OTH
AF:
0.306
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.344
AC:
52079
AN:
151320
Hom.:
10047
Cov.:
28
AF XY:
0.340
AC XY:
25155
AN XY:
73910
show subpopulations
African (AFR)
AF:
0.525
AC:
21643
AN:
41190
American (AMR)
AF:
0.272
AC:
4143
AN:
15204
Ashkenazi Jewish (ASJ)
AF:
0.264
AC:
915
AN:
3464
East Asian (EAS)
AF:
0.203
AC:
1041
AN:
5116
South Asian (SAS)
AF:
0.231
AC:
1104
AN:
4788
European-Finnish (FIN)
AF:
0.299
AC:
3117
AN:
10442
Middle Eastern (MID)
AF:
0.221
AC:
65
AN:
294
European-Non Finnish (NFE)
AF:
0.284
AC:
19265
AN:
67814
Other (OTH)
AF:
0.302
AC:
634
AN:
2100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1565
3130
4696
6261
7826
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
498
996
1494
1992
2490
<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:
0.272
Hom.:
1007

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.32
DANN
Benign
0.76
PhyloP100
-1.0
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: rs6984928; hg19: chr8-124154275; API