NM_001145418.2:c.103-9146G>A

Variant names:

• chr22-28638976-C-T
• rs5752764
• NM_001145418.2:c.103-9146G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145418.2(TTC28):​c.103-9146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,038 control chromosomes in the GnomAD database, including 27,040 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 0.59 (27040 hom., cov: 32)
• Consequence: TTC28 NM_001145418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 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.103-9146G>A		intron	N/A	NP_001138890.1
	TTC28	NM_001393403.1		c.103-9146G>A		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.103-9146G>A		intron	N/A	ENSP00000381003.2
	TTC28	ENST00000468807.1	TSL:2	n.192-9146G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89614 AN: 151920 Hom.: 27031 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.590 AC: 89654 AN: 152038 Hom.: 27040 Cov.: 32 AF XY: 0.591 AC XY: 43910 AN XY: 74322

African (AFR) AF: 0.459 AC: 19022 AN: 41438

American (AMR) AF: 0.574 AC: 8767 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2424 AN: 3470

East Asian (EAS) AF: 0.624 AC: 3227 AN: 5174

South Asian (SAS) AF: 0.737 AC: 3553 AN: 4824

European-Finnish (FIN) AF: 0.650 AC: 6858 AN: 10558

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43686 AN: 67986

Other (OTH) AF: 0.613 AC: 1294 AN: 2112

Alfa AF: 0.562 Hom.: 6585

Bravo AF: 0.578

Asia WGS AF: 0.709 AC: 2467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.98
DANN	Benign	0.20
PhyloP100		-0.17
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: rs5752764; hg19: chr22-29034964;