X-12906102-T-C

Position:

• chrX-12906102-T-C

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+88A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 29 control chromosomes in the GnomAD database, including 1 homozygotes. There are 16 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 0.72 (20564 hom., 24019 hem., cov: 23)
  • Exomes 𝑓: 0.69 (1 hom. 16 hem.)
  • Failed GnomAD Quality Control
• Consequence: TLR8-AS1 NR_030727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.93).
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLR8-AS1	NR_030727.1	n.420+88A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TLR8-AS1	ENST00000451564.1	n.180+88A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.721 AC: 80013 AN: 110990 Hom.: 20573 Cov.: 23 AF XY: 0.723 AC XY: 23974 AN XY: 33176

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.735

GnomAD4 exome AF: 0.690 AC: 20 AN: 29 Hom.: 1 AF XY: 0.696 AC XY: 16 AN XY: 23

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.640

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.721 AC: 80047 AN: 111043 Hom.: 20564 Cov.: 23 AF XY: 0.723 AC XY: 24019 AN XY: 33239

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.736

Alfa AF: 0.714 Hom.: 10523

Bravo AF: 0.723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.040
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5741883; hg19: chrX-12924221;