rs5752764

chr22-28638976-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC28	NM_001145418.2	c.103-9146G>A		intron_variant		ENST00000397906.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC28	ENST00000397906.7	c.103-9146G>A		intron_variant		1	NM_001145418.2	P1
TTC28	ENST00000468807.1	n.192-9146G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.613

Alfa AF: 0.614 Hom.: 5034

Bravo AF: 0.578

Asia WGS AF: 0.709 AC: 2467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.98
Dann	Benign	0.20

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: rs5752764; hg19: chr22-29034964;