11-43398360-A-G

Variant names:

• chr11-43398360-A-G
• rs17508783
• NM_018259.6:c.1058+247A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018259.6. 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
	TTC17	NM_018259.6	MANE Select	c.1058+247A>G		intron	N/A	NP_060729.2
	TTC17	NM_001376525.1		c.1058+247A>G		intron	N/A	NP_001363454.1
	TTC17	NM_001376526.1		c.968+247A>G		intron	N/A	NP_001363455.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTC17	ENST00000039989.9	TSL:1 MANE Select	c.1058+247A>G		intron	N/A	ENSP00000039989.4
	TTC17	ENST00000299240.10	TSL:1	c.1058+247A>G		intron	N/A	ENSP00000299240.5
	TTC17	ENST00000526774.5	TSL:1	n.968+247A>G		intron	N/A

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

African (AFR) AF: 0.0425 AC: 1767 AN: 41554

American (AMR) AF: 0.142 AC: 2174 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3468

East Asian (EAS) AF: 0.107 AC: 553 AN: 5170

South Asian (SAS) AF: 0.0761 AC: 367 AN: 4824

European-Finnish (FIN) AF: 0.311 AC: 3288 AN: 10576

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16333 AN: 67982

Other (OTH) AF: 0.192 AC: 406 AN: 2114

Alfa AF: 0.210 Hom.: 1871

Bravo AF: 0.154

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.7
DANN	Benign	0.87
PhyloP100		-0.17
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: rs17508783; hg19: chr11-43419910;