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GeneBe

17-82752223-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_005993.5(TBCD):c.30C>T(p.Gly10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0202 in 1,524,226 control chromosomes in the GnomAD database, including 377 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 30 hom., cov: 33)
Exomes 𝑓: 0.021 ( 347 hom. )

Consequence

TBCD
NM_005993.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.200
Variant links:
Genes affected
TBCD (HGNC:11581): (tubulin folding cofactor D) Cofactor D is one of four proteins (cofactors A, D, E, and C) involved in the pathway leading to correctly folded beta-tubulin from folding intermediates. Cofactors A and D are believed to play a role in capturing and stabilizing beta-tubulin intermediates in a quasi-native confirmation. Cofactor E binds to the cofactor D/beta-tubulin complex; interaction with cofactor C then causes the release of beta-tubulin polypeptides that are committed to the native state. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-82752223-C-T is Benign according to our data. Variant chr17-82752223-C-T is described in ClinVar as [Benign]. Clinvar id is 1570656.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.2 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0152 (2311/152248) while in subpopulation EAS AF= 0.0272 (141/5176). AF 95% confidence interval is 0.0236. There are 30 homozygotes in gnomad4. There are 1158 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 30 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TBCDNM_005993.5 linkuse as main transcriptc.30C>T p.Gly10= synonymous_variant 1/39 ENST00000355528.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TBCDENST00000355528.9 linkuse as main transcriptc.30C>T p.Gly10= synonymous_variant 1/391 NM_005993.5 P1Q9BTW9-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0152
AC:
2314
AN:
152134
Hom.:
30
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00362
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00929
Gnomad ASJ
AF:
0.0147
Gnomad EAS
AF:
0.0273
Gnomad SAS
AF:
0.00620
Gnomad FIN
AF:
0.0333
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.0208
Gnomad OTH
AF:
0.0153
GnomAD3 exomes
AF:
0.0164
AC:
1887
AN:
115256
Hom.:
20
AF XY:
0.0162
AC XY:
1037
AN XY:
63890
show subpopulations
Gnomad AFR exome
AF:
0.00113
Gnomad AMR exome
AF:
0.00517
Gnomad ASJ exome
AF:
0.0179
Gnomad EAS exome
AF:
0.0310
Gnomad SAS exome
AF:
0.00665
Gnomad FIN exome
AF:
0.0352
Gnomad NFE exome
AF:
0.0212
Gnomad OTH exome
AF:
0.0111
GnomAD4 exome
AF:
0.0207
AC:
28434
AN:
1371978
Hom.:
347
Cov.:
31
AF XY:
0.0203
AC XY:
13722
AN XY:
676988
show subpopulations
Gnomad4 AFR exome
AF:
0.00266
Gnomad4 AMR exome
AF:
0.00576
Gnomad4 ASJ exome
AF:
0.0167
Gnomad4 EAS exome
AF:
0.0450
Gnomad4 SAS exome
AF:
0.00644
Gnomad4 FIN exome
AF:
0.0336
Gnomad4 NFE exome
AF:
0.0218
Gnomad4 OTH exome
AF:
0.0172
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0152
AC:
2311
AN:
152248
Hom.:
30
Cov.:
33
AF XY:
0.0156
AC XY:
1158
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.00361
Gnomad4 AMR
AF:
0.00928
Gnomad4 ASJ
AF:
0.0147
Gnomad4 EAS
AF:
0.0272
Gnomad4 SAS
AF:
0.00579
Gnomad4 FIN
AF:
0.0333
Gnomad4 NFE
AF:
0.0208
Gnomad4 OTH
AF:
0.0151
Alfa
AF:
0.0173
Hom.:
10
Bravo
AF:
0.0130
Asia WGS
AF:
0.0120
AC:
40
AN:
3474

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 31, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
Cadd
Benign
10
Dann
Benign
0.87
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs11550067; hg19: chr17-80710099; COSMIC: COSV56182363; COSMIC: COSV56182363; API