rs17508783

chr11-43398360-A-G

Variant summary

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

The NM_018259.6(TTC17):c.1058+247A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,186 control chromosomes in the GnomAD database, including 2,934 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 0.17 (2934 hom., cov: 32)
• Consequence: TTC17 NM_018259.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

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=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTC17	NM_018259.6	c.1058+247A>G		intron_variant		ENST00000039989.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTC17	ENST00000039989.9	c.1058+247A>G		intron_variant		1	NM_018259.6	A1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26033 AN: 152068 Hom.: 2932 Cov.: 32

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0758

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.171 AC: 26041 AN: 152186 Hom.: 2934 Cov.: 32 AF XY: 0.170 AC XY: 12667 AN XY: 74386

Gnomad4 AFR AF: 0.0425

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0761

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.192

Alfa AF: 0.210 Hom.: 1672

Bravo AF: 0.154

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	2.7
Dann	Benign	0.87

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: rs17508783; hg19: chr11-43419910;