ENST00000451564.1:n.181-555T>C

Variant names:

• chrX-12904540-A-G
• rs3788935
• ENST00000451564.1:n.181-555T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000451564.1(TLR8-AS1):​n.181-555T>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 ENST00000451564.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 18 publications found

Genes affected

TLR8-AS1 (HGNC:40720): (TLR8 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451564.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR8-AS1	NR_030727.1		n.421-555T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR8-AS1	ENST00000451564.1	TSL:5	n.181-555T>C		intron	N/A

Frequencies

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

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

African (AFR) AF: 0.253 AC: 7615 AN: 30156

American (AMR) AF: 0.452 AC: 4629 AN: 10251

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1055 AN: 2619

East Asian (EAS) AF: 0.808 AC: 2817 AN: 3485

South Asian (SAS) AF: 0.517 AC: 1331 AN: 2575

European-Finnish (FIN) AF: 0.202 AC: 1159 AN: 5751

Middle Eastern (MID) AF: 0.366 AC: 78 AN: 213

European-Non Finnish (NFE) AF: 0.254 AC: 13388 AN: 52693

Other (OTH) AF: 0.336 AC: 497 AN: 1478

Alfa AF: 0.265 Hom.: 9117

Bravo AF: 0.324

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.2
DANN	Benign	0.53
PhyloP100		0.32

Splicing

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

Other links and lift over

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