rs6005834

Variant names:

• chr22-28679138-T-C
• rs6005834
• NM_001145418.2:c.102+484A>G

Variant summary

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

The NM_001145418.2(TTC28):​c.102+484A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.086 in 152,270 control chromosomes in the GnomAD database, including 1,007 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 0.086 (1007 hom., cov: 32)
• Consequence: TTC28 NM_001145418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 3 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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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.102+484A>G		intron	N/A	NP_001138890.1
	TTC28	NM_001393403.1		c.102+484A>G		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.102+484A>G		intron	N/A	ENSP00000381003.2
	TTC28	ENST00000468807.1	TSL:2	n.191+484A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0858 AC: 13059 AN: 152152 Hom.: 1000 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0439

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.0538

Gnomad SAS AF: 0.0437

Gnomad FIN AF: 0.0616

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0354

Gnomad OTH AF: 0.0640

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

GnomAD4 genome AF: 0.0860 AC: 13090 AN: 152270 Hom.: 1007 Cov.: 32 AF XY: 0.0863 AC XY: 6428 AN XY: 74466

African (AFR) AF: 0.207 AC: 8591 AN: 41536

American (AMR) AF: 0.0438 AC: 671 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3472

East Asian (EAS) AF: 0.0536 AC: 277 AN: 5172

South Asian (SAS) AF: 0.0440 AC: 212 AN: 4820

European-Finnish (FIN) AF: 0.0616 AC: 654 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0355 AC: 2412 AN: 68022

Other (OTH) AF: 0.0647 AC: 137 AN: 2116

Alfa AF: 0.0670 Hom.: 94

Bravo AF: 0.0897

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.96
DANN	Benign	0.54
PhyloP100		-0.99
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: rs6005834; hg19: chr22-29075126;