rs3761624

Variant names:

• chrX-12905562-A-G
• rs3761624
• ENST00000451564.1:n.180+628T>C

Variant summary

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

The NR_030727.1(TLR8-AS1):​n.420+628T>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 111,635 control chromosomes in the GnomAD database, including 3,978 homozygotes. There are 10,212 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., 10212 hem., cov: 23)
• Consequence: TLR8-AS1 NR_030727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 32 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_030727.1. 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.420+628T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR8-AS1	ENST00000451564.1	TSL:5	n.180+628T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 33359 AN: 111581 Hom.: 3981 Cov.: 23

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.371

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.299 AC: 33385 AN: 111635 Hom.: 3978 Cov.: 23 AF XY: 0.302 AC XY: 10212 AN XY: 33841

African (AFR) AF: 0.255 AC: 7846 AN: 30737

American (AMR) AF: 0.452 AC: 4751 AN: 10522

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1069 AN: 2641

East Asian (EAS) AF: 0.809 AC: 2870 AN: 3547

South Asian (SAS) AF: 0.522 AC: 1395 AN: 2674

European-Finnish (FIN) AF: 0.197 AC: 1181 AN: 6002

Middle Eastern (MID) AF: 0.366 AC: 79 AN: 216

European-Non Finnish (NFE) AF: 0.253 AC: 13424 AN: 53105

Other (OTH) AF: 0.338 AC: 513 AN: 1518

Alfa AF: 0.274 Hom.: 6029

Bravo AF: 0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.71
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs3761624; hg19: chrX-12923681;