rs6005834

chr22-28679138-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC28	NM_001145418.2	c.102+484A>G		intron_variant		ENST00000397906.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC28	ENST00000397906.7	c.102+484A>G		intron_variant		1	NM_001145418.2	P1
TTC28	ENST00000468807.1	n.191+484A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.0438

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.0536

Gnomad4 SAS AF: 0.0440

Gnomad4 FIN AF: 0.0616

Gnomad4 NFE AF: 0.0355

Gnomad4 OTH AF: 0.0647

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	0.96
Dann	Benign	0.54

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: rs6005834; hg19: chr22-29075126;