NM_001145418.2:c.382-142648T>C

Variant names:

• chr22-28449291-A-G
• rs5762629
• NM_001145418.2:c.382-142648T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145418.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC28	NM_001145418.2	MANE Select	c.382-142648T>C		intron	N/A	NP_001138890.1
	TTC28	NM_001393403.1		c.382-142648T>C		intron	N/A	NP_001380332.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC28	ENST00000397906.7	TSL:1 MANE Select	c.382-142648T>C		intron	N/A	ENSP00000381003.2

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

African (AFR) AF: 0.477 AC: 19791 AN: 41464

American (AMR) AF: 0.725 AC: 11071 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2787 AN: 3468

East Asian (EAS) AF: 0.636 AC: 3279 AN: 5154

South Asian (SAS) AF: 0.790 AC: 3812 AN: 4828

European-Finnish (FIN) AF: 0.696 AC: 7374 AN: 10596

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.718 AC: 48818 AN: 67956

Other (OTH) AF: 0.674 AC: 1425 AN: 2114

Alfa AF: 0.704 Hom.: 22770

Bravo AF: 0.643

Asia WGS AF: 0.740 AC: 2577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.77
PhyloP100		-0.089
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5762629; hg19: chr22-28845279;