rs695388

Variant names:

• chr22-28437514-C-A
• rs695388
• NM_001145418.2:c.382-130871G>T

Your query was ambiguous. Multiple possible variants found:

• chr22-28437514-C-A
• chr22-28437514-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145418.2(TTC28):​c.382-130871G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,040 control chromosomes in the GnomAD database, including 17,146 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 0.47 (17146 hom., cov: 32)
• Consequence: TTC28 NM_001145418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• 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 = 0.526 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145418.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC28	NM_001145418.2	MANE Select	c.382-130871G>T		intron	N/A	NP_001138890.1
	TTC28	NM_001393403.1		c.382-130871G>T		intron	N/A	NP_001380332.1
	TTC28	NM_001393404.1		c.27+5372G>T		intron	N/A	NP_001380333.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC28	ENST00000397906.7	TSL:1 MANE Select	c.382-130871G>T		intron	N/A	ENSP00000381003.2
	TTC28	ENST00000490475.1	TSL:5	n.188+5372G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71069 AN: 151922 Hom.: 17139 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.468 AC: 71097 AN: 152040 Hom.: 17146 Cov.: 32 AF XY: 0.465 AC XY: 34565 AN XY: 74296

African (AFR) AF: 0.396 AC: 16428 AN: 41458

American (AMR) AF: 0.348 AC: 5311 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1438 AN: 3466

East Asian (EAS) AF: 0.346 AC: 1788 AN: 5162

South Asian (SAS) AF: 0.536 AC: 2583 AN: 4818

European-Finnish (FIN) AF: 0.565 AC: 5965 AN: 10556

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36061 AN: 67990

Other (OTH) AF: 0.448 AC: 944 AN: 2108

Alfa AF: 0.506 Hom.: 21681

Bravo AF: 0.445

Asia WGS AF: 0.464 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.64
PhyloP100		-0.023
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: rs695388; hg19: chr22-28833502;