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GeneBe

rs10985528

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001267571.2(TBC1D2):c.978+132T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0831 in 799,394 control chromosomes in the GnomAD database, including 3,177 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 0.076 ( 564 hom., cov: 33)
Exomes 𝑓: 0.085 ( 2613 hom. )

Consequence

TBC1D2
NM_001267571.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.95
Variant links:
Genes affected
TBC1D2 (HGNC:18026): (TBC1 domain family member 2) Enables GTPase activator activity and cadherin binding activity. Involved in positive regulation of GTPase activity. Located in several cellular components, including cytoplasmic vesicle; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.097 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TBC1D2NM_001267571.2 linkuse as main transcriptc.978+132T>G intron_variant ENST00000465784.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TBC1D2ENST00000465784.7 linkuse as main transcriptc.978+132T>G intron_variant 1 NM_001267571.2 P2Q9BYX2-1

Frequencies

GnomAD3 genomes
AF:
0.0764
AC:
11619
AN:
152150
Hom.:
564
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0439
Gnomad AMI
AF:
0.236
Gnomad AMR
AF:
0.0553
Gnomad ASJ
AF:
0.163
Gnomad EAS
AF:
0.000962
Gnomad SAS
AF:
0.0640
Gnomad FIN
AF:
0.0868
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.0990
Gnomad OTH
AF:
0.0833
GnomAD4 exome
AF:
0.0847
AC:
54822
AN:
647126
Hom.:
2613
AF XY:
0.0850
AC XY:
28555
AN XY:
335770
show subpopulations
Gnomad4 AFR exome
AF:
0.0430
Gnomad4 AMR exome
AF:
0.0480
Gnomad4 ASJ exome
AF:
0.159
Gnomad4 EAS exome
AF:
0.000369
Gnomad4 SAS exome
AF:
0.0632
Gnomad4 FIN exome
AF:
0.0940
Gnomad4 NFE exome
AF:
0.0942
Gnomad4 OTH exome
AF:
0.0877
GnomAD4 genome
AF:
0.0764
AC:
11627
AN:
152268
Hom.:
564
Cov.:
33
AF XY:
0.0747
AC XY:
5559
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.0442
Gnomad4 AMR
AF:
0.0552
Gnomad4 ASJ
AF:
0.163
Gnomad4 EAS
AF:
0.000964
Gnomad4 SAS
AF:
0.0634
Gnomad4 FIN
AF:
0.0868
Gnomad4 NFE
AF:
0.0990
Gnomad4 OTH
AF:
0.0819
Alfa
AF:
0.0922
Hom.:
88
Bravo
AF:
0.0708
Asia WGS
AF:
0.0320
AC:
113
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
Cadd
Benign
7.6
Dann
Benign
0.44

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10985528; hg19: chr9-100991102; API