chrX-12904540-A-G

Position:

• chrX-12904540-A-G

Variant summary

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

The NR_030727.1(TLR8-AS1):​n.421-555T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 109,889 control chromosomes in the GnomAD database, including 3,978 homozygotes. There are 9,633 hemizygotes in GnomAD. 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 0.30 (3978 hom., 9633 hem., cov: 22)
• Consequence: TLR8-AS1 NR_030727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316

Genes affected

TLR8-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLR8-AS1	NR_030727.1	n.421-555T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TLR8-AS1	ENST00000451564.1	n.181-555T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.299 AC: 32799 AN: 109833 Hom.: 3981 Cov.: 22 AF XY: 0.299 AC XY: 9607 AN XY: 32097

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.368

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.299 AC: 32824 AN: 109889 Hom.: 3978 Cov.: 22 AF XY: 0.300 AC XY: 9633 AN XY: 32163

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.336

Alfa AF: 0.252 Hom.: 5931

Bravo AF: 0.324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3788935; hg19: chrX-12922659; COSMIC: COSV54321491;