rs5762629

chr22-28449291-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145418.2(TTC28):c.382-142648T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,058 control chromosomes in the GnomAD database, including 33,383 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 0.65 (33383 hom., cov: 32)
• Consequence: TTC28 NM_001145418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC28	NM_001145418.2	c.382-142648T>C		intron_variant		ENST00000397906.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC28	ENST00000397906.7	c.382-142648T>C		intron_variant		1	NM_001145418.2	P1

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99171 AN: 151942 Hom.: 33380 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.677

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.652 AC: 99206 AN: 152058 Hom.: 33383 Cov.: 32 AF XY: 0.655 AC XY: 48653 AN XY: 74326

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.674

Alfa AF: 0.691 Hom.: 9460

Bravo AF: 0.643

Asia WGS AF: 0.740 AC: 2577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.77

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

Other links and lift over

dbSNP: rs5762629; hg19: chr22-28845279;