rs17429273

Positions:

• chr4-38867279-A-G

Variant summary

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

The XM_047449498.1(TLR6):​c.-65+647T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,214 control chromosomes in the GnomAD database, including 3,995 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 0.20 (3995 hom., cov: 32)
• Consequence: TLR6 XM_047449498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401

Genes affected

TLR6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLR6	XM_047449498.1	c.-65+647T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31125 AN: 152096 Hom.: 3993 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0140

Gnomad SAS AF: 0.0925

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.205 AC: 31133 AN: 152214 Hom.: 3995 Cov.: 32 AF XY: 0.201 AC XY: 14932 AN XY: 74410

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0142

Gnomad4 SAS AF: 0.0921

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.174

Alfa AF: 0.234 Hom.: 1649

Bravo AF: 0.183

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17429273; hg19: chr4-38868900;