rs17509647

Positions:

• chr11-43451557-T-C

Variant summary

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

The NM_018259.6(TTC17):​c.3030+292T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 152,260 control chromosomes in the GnomAD database, including 566 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 0.070 (566 hom., cov: 32)
• Consequence: TTC17 NM_018259.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582

Genes affected

TTC17 (HGNC:25596): (tetratricopeptide repeat domain 17) Involved in actin filament polymerization and cilium organization. Located in actin cytoskeleton; cytosol; and plasma membrane. [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 (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC17	NM_018259.6	c.3030+292T>C		intron_variant		ENST00000039989.9	NP_060729.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC17	ENST00000039989.9	c.3030+292T>C		intron_variant		1	NM_018259.6	ENSP00000039989	A1

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10685 AN: 152142 Hom.: 566 Cov.: 32

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0534

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0702 AC: 10686 AN: 152260 Hom.: 566 Cov.: 32 AF XY: 0.0690 AC XY: 5135 AN XY: 74444

Gnomad4 AFR AF: 0.0169

Gnomad4 AMR AF: 0.0533

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0638

Alfa AF: 0.0897 Hom.: 970

Bravo AF: 0.0601

Asia WGS AF: 0.0120 AC: 42 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	14
DANN	Benign	0.85

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: rs17509647; hg19: chr11-43473107;