rs13058493

Variant summary

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

The NM_001145418.2(TTC28):​c.3547+147A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0575 in 1,025,890 control chromosomes in the GnomAD database, including 2,234 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 0.077 ( 659 hom., cov: 32)
Exomes 𝑓: 0.054 ( 1575 hom. )

Consequence

TTC28
NM_001145418.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.387
Variant links:
Genes affected
TTC28 (HGNC:29179): (tetratricopeptide repeat domain 28) Enables kinase binding activity. Involved in regulation of mitotic cell cycle. Located in midbody. [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=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TTC28NM_001145418.2 linkc.3547+147A>G intron_variant ENST00000397906.7 NP_001138890.1 Q96AY4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TTC28ENST00000397906.7 linkc.3547+147A>G intron_variant 1 NM_001145418.2 ENSP00000381003.2 Q96AY4
TTC28ENST00000612946.4 linkc.3166+147A>G intron_variant 5 ENSP00000479834.1 A0A087WW06

Frequencies

GnomAD3 genomes
AF:
0.0768
AC:
11689
AN:
152148
Hom.:
654
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.146
Gnomad AMI
AF:
0.0746
Gnomad AMR
AF:
0.0371
Gnomad ASJ
AF:
0.0331
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0567
Gnomad FIN
AF:
0.0711
Gnomad MID
AF:
0.0443
Gnomad NFE
AF:
0.0542
Gnomad OTH
AF:
0.0675
GnomAD4 exome
AF:
0.0541
AC:
47274
AN:
873624
Hom.:
1575
AF XY:
0.0541
AC XY:
23692
AN XY:
437838
show subpopulations
Gnomad4 AFR exome
AF:
0.151
Gnomad4 AMR exome
AF:
0.0308
Gnomad4 ASJ exome
AF:
0.0422
Gnomad4 EAS exome
AF:
0.000154
Gnomad4 SAS exome
AF:
0.0577
Gnomad4 FIN exome
AF:
0.0659
Gnomad4 NFE exome
AF:
0.0539
Gnomad4 OTH exome
AF:
0.0528
GnomAD4 genome
AF:
0.0769
AC:
11712
AN:
152266
Hom.:
659
Cov.:
32
AF XY:
0.0751
AC XY:
5591
AN XY:
74462
show subpopulations
Gnomad4 AFR
AF:
0.147
Gnomad4 AMR
AF:
0.0371
Gnomad4 ASJ
AF:
0.0331
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0569
Gnomad4 FIN
AF:
0.0711
Gnomad4 NFE
AF:
0.0542
Gnomad4 OTH
AF:
0.0668
Alfa
AF:
0.0570
Hom.:
244
Bravo
AF:
0.0767
Asia WGS
AF:
0.0250
AC:
85
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.33
DANN
Benign
0.79

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: rs13058493; hg19: chr22-28494756; API