rs6005835

chr22-28679331-G-Cchr22-28679331-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.102+291C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,160 control chromosomes in the GnomAD database, including 44,809 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 0.77 (44809 hom., cov: 35)
• Consequence: TTC28 NM_001145418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC28	NM_001145418.2	c.102+291C>G		intron_variant		ENST00000397906.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC28	ENST00000397906.7	c.102+291C>G		intron_variant		1	NM_001145418.2	P1
TTC28	ENST00000468807.1	n.191+291C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116437 AN: 152042 Hom.: 44775 Cov.: 35

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.766 AC: 116523 AN: 152160 Hom.: 44809 Cov.: 35 AF XY: 0.768 AC XY: 57132 AN XY: 74390

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.760

Alfa AF: 0.769 Hom.: 5604

Bravo AF: 0.764

Asia WGS AF: 0.828 AC: 2881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.2
Dann	Benign	0.44

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: rs6005835; hg19: chr22-29075319;