rs3761624

Positions:

• chrX-12905562-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.420+628T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLR8-AS1	NR_030727.1	n.420+628T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TLR8-AS1	ENST00000451564.1	n.180+628T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.299 AC: 33359 AN: 111581 Hom.: 3981 Cov.: 23 AF XY: 0.302 AC XY: 10185 AN XY: 33777

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

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.338

Alfa AF: 0.272 Hom.: 4250

Bravo AF: 0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761624; hg19: chrX-12923681;