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GeneBe

6-158429867-G-A

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7

The NM_020245.5(TULP4):c.513G>A(p.Thr171=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00043 in 1,613,996 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00035 ( 1 hom. )

Consequence

TULP4
NM_020245.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.86
Variant links:
Genes affected
TULP4 (HGNC:15530): (TUB like protein 4) Predicted to be involved in protein ubiquitination. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
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=-0.46).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-158429867-G-A is Benign according to our data. Variant chr6-158429867-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2657085.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=-1.86 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TULP4NM_020245.5 linkuse as main transcriptc.513G>A p.Thr171= synonymous_variant 3/14 ENST00000367097.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TULP4ENST00000367097.8 linkuse as main transcriptc.513G>A p.Thr171= synonymous_variant 3/141 NM_020245.5 P1Q9NRJ4-1
TULP4ENST00000367094.6 linkuse as main transcriptc.513G>A p.Thr171= synonymous_variant 3/131 Q9NRJ4-2
TULP4ENST00000616856.1 linkuse as main transcriptn.1085G>A non_coding_transcript_exon_variant 3/82

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00121
AC:
184
AN:
152078
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00362
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000328
Gnomad ASJ
AF:
0.00289
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000221
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.000621
AC:
156
AN:
251320
Hom.:
0
AF XY:
0.000545
AC XY:
74
AN XY:
135834
show subpopulations
Gnomad AFR exome
AF:
0.00332
Gnomad AMR exome
AF:
0.000782
Gnomad ASJ exome
AF:
0.00258
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.000261
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000317
Gnomad OTH exome
AF:
0.000489
GnomAD4 exome
AF:
0.000350
AC:
511
AN:
1461800
Hom.:
1
Cov.:
30
AF XY:
0.000349
AC XY:
254
AN XY:
727190
show subpopulations
Gnomad4 AFR exome
AF:
0.00332
Gnomad4 AMR exome
AF:
0.000761
Gnomad4 ASJ exome
AF:
0.00249
Gnomad4 EAS exome
AF:
0.000126
Gnomad4 SAS exome
AF:
0.000325
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000186
Gnomad4 OTH exome
AF:
0.000745
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00120
AC:
183
AN:
152196
Hom.:
0
Cov.:
33
AF XY:
0.00110
AC XY:
82
AN XY:
74398
show subpopulations
Gnomad4 AFR
AF:
0.00361
Gnomad4 AMR
AF:
0.000327
Gnomad4 ASJ
AF:
0.00289
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000221
Gnomad4 OTH
AF:
0.000948
Alfa
AF:
0.00121
Hom.:
0
Bravo
AF:
0.00131
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.000600
EpiControl
AF:
0.000771

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenOct 01, 2022TULP4: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
Cadd
Benign
1.1
Dann
Benign
0.80
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: rs138932674; hg19: chr6-158850899; API