rs134547

Positions:

• chr22-28405021-G-A
• chr22-28405021-G-C
• chr22-28405021-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145418.2(TTC28):​c.382-98378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,154 control chromosomes in the GnomAD database, including 56,660 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 0.86 (56660 hom., cov: 31)
• Consequence: TTC28 NM_001145418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC28	NM_001145418.2	c.382-98378C>T		intron_variant		ENST00000397906.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC28	ENST00000397906.7	c.382-98378C>T		intron_variant		1	NM_001145418.2	P1
TTC28	ENST00000490475.1	n.188+37865C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130925 AN: 152036 Hom.: 56626 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.951

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.861 AC: 131010 AN: 152154 Hom.: 56660 Cov.: 31 AF XY: 0.862 AC XY: 64083 AN XY: 74384

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.951

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.895

Alfa AF: 0.869 Hom.: 15761

Bravo AF: 0.866

Asia WGS AF: 0.930 AC: 3233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.3
DANN	Benign	0.66

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: rs134547; hg19: chr22-28801009;