rs9613617

Variant names:

• chr22-28451908-T-C
• rs9613617
• NM_001145418.2:c.382-145265A>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.382-145265A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,064 control chromosomes in the GnomAD database, including 7,517 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 0.28 (7517 hom., cov: 32)
• Consequence: TTC28 NM_001145418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 4 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 = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC28	NM_001145418.2	c.382-145265A>G		intron_variant	Intron 2 of 22	ENST00000397906.7	NP_001138890.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTC28	ENST00000397906.7	c.382-145265A>G		intron_variant	Intron 2 of 22	1	NM_001145418.2	ENSP00000381003.2

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43094 AN: 151946 Hom.: 7525 Cov.: 32

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.283 AC: 43075 AN: 152064 Hom.: 7517 Cov.: 32 AF XY: 0.283 AC XY: 21022 AN XY: 74298

African (AFR) AF: 0.0782 AC: 3247 AN: 41522

American (AMR) AF: 0.240 AC: 3668 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1230 AN: 3468

East Asian (EAS) AF: 0.260 AC: 1340 AN: 5162

South Asian (SAS) AF: 0.401 AC: 1929 AN: 4814

European-Finnish (FIN) AF: 0.383 AC: 4039 AN: 10546

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26531 AN: 67964

Other (OTH) AF: 0.301 AC: 635 AN: 2110

Alfa AF: 0.356 Hom.: 5996

Bravo AF: 0.263

Asia WGS AF: 0.353 AC: 1230 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	3.2
DANN	Benign	0.76
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: rs9613617; hg19: chr22-28847896;