rs534611598

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS1

The NM_001199107.2(TBC1D24):​c.-116+73C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0333 in 60 control chromosomes in the GnomAD database, including 1 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: not found (cov: 33)
Exomes 𝑓: 0.033 ( 1 hom. )

Consequence

TBC1D24
NM_001199107.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.00
Variant links:
Genes affected
TBC1D24 (HGNC:29203): (TBC1 domain family member 24) This gene encodes a protein with a conserved domain, referred to as the TBC domain, characteristic of proteins which interact with GTPases. TBC domain proteins may serve as GTPase-activating proteins for a particular group of GTPases, the Rab (Ras-related proteins in brain) small GTPases which are involved in the regulation of membrane trafficking. Mutations in this gene are associated with familial infantile myoclonic epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BS1
Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.0333 (2/60) while in subpopulation SAS AF= 0.0345 (2/58). AF 95% confidence interval is 0.00613. There are 1 homozygotes in gnomad4_exome. There are 0 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TBC1D24NM_001199107.2 linkc.-116+73C>G intron_variant Intron 1 of 7 ENST00000646147.1 NP_001186036.1 Q9ULP9-1
TBC1D24NM_020705.3 linkc.-116+73C>G intron_variant Intron 1 of 6 NP_065756.1 Q9ULP9-2
TBC1D24XM_017023493.2 linkc.-116+73C>G intron_variant Intron 1 of 8 XP_016878982.1 Q9ULP9-1
TBC1D24XM_017023495.2 linkc.-116+73C>G intron_variant Intron 1 of 7 XP_016878984.1 Q9ULP9-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TBC1D24ENST00000646147.1 linkc.-116+73C>G intron_variant Intron 1 of 7 NM_001199107.2 ENSP00000494678.1 Q9ULP9-1
TBC1D24ENST00000567020.6 linkc.-116+73C>G intron_variant Intron 1 of 6 1 ENSP00000454408.1 Q9ULP9-2
TBC1D24ENST00000569874.2 linkn.-116+73C>G intron_variant Intron 1 of 7 5 ENSP00000455005.2 Q9ULP9-2
TBC1D24ENST00000630263.2 linkn.-142+73C>G intron_variant Intron 1 of 7 5 ENSP00000486835.1 A0A0D9SFR5

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.0333
AC:
2
AN:
60
Hom.:
1
AF XY:
0.00
AC XY:
0
AN XY:
34
show subpopulations
Gnomad4 SAS exome
AF:
0.0345
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.4
DANN
Benign
0.25

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-2525244; API