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GeneBe

17-59890847-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_016261.4(TUBD1):c.156T>C(p.Ser52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00444 in 1,612,772 control chromosomes in the GnomAD database, including 272 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.023 ( 128 hom., cov: 32)
Exomes 𝑓: 0.0025 ( 144 hom. )

Consequence

TUBD1
NM_016261.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0480
Variant links:
Genes affected
TUBD1 (HGNC:16811): (tubulin delta 1) Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization; mitotic cell cycle; and positive regulation of smoothened signaling pathway. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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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=-0.59).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-59890847-A-G is Benign according to our data. Variant chr17-59890847-A-G is described in ClinVar as [Benign]. Clinvar id is 778719.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=0.048 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0758 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TUBD1NM_016261.4 linkuse as main transcriptc.156T>C p.Ser52= synonymous_variant 2/9 ENST00000325752.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TUBD1ENST00000325752.8 linkuse as main transcriptc.156T>C p.Ser52= synonymous_variant 2/95 NM_016261.4 P1Q9UJT1-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0225
AC:
3427
AN:
152142
Hom.:
125
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0776
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00930
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.000309
Gnomad OTH
AF:
0.0196
GnomAD3 exomes
AF:
0.00615
AC:
1535
AN:
249540
Hom.:
47
AF XY:
0.00443
AC XY:
598
AN XY:
134936
show subpopulations
Gnomad AFR exome
AF:
0.0809
Gnomad AMR exome
AF:
0.00453
Gnomad ASJ exome
AF:
0.000100
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000263
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000302
Gnomad OTH exome
AF:
0.00394
GnomAD4 exome
AF:
0.00254
AC:
3711
AN:
1460512
Hom.:
144
Cov.:
31
AF XY:
0.00222
AC XY:
1611
AN XY:
726550
show subpopulations
Gnomad4 AFR exome
AF:
0.0876
Gnomad4 AMR exome
AF:
0.00519
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000325
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000110
Gnomad4 OTH exome
AF:
0.00592
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0227
AC:
3456
AN:
152260
Hom.:
128
Cov.:
32
AF XY:
0.0216
AC XY:
1605
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.0781
Gnomad4 AMR
AF:
0.00929
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000309
Gnomad4 OTH
AF:
0.0194
Alfa
AF:
0.00973
Hom.:
21
Bravo
AF:
0.0268
Asia WGS
AF:
0.00866
AC:
30
AN:
3478
EpiCase
AF:
0.000491
EpiControl
AF:
0.000475

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 testingInvitaeJul 05, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.59
Cadd
Benign
7.4
Dann
Benign
0.84
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs76112765; hg19: chr17-57968208; API