X-12906102-T-C

Variant names:

• chrX-12906102-T-C
• rs5741883
• ENST00000451564.1:n.180+88A>G

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+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
• Publications: 24 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: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 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+88A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TLR8-AS1	ENST00000451564.1	TSL:5	n.180+88A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.721 AC: 80013 AN: 110990 Hom.: 20573 Cov.: 23

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 1 AN: 1

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 3 AN: 3

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.640 AC: 16 AN: 25

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.594 AC: 18123 AN: 30529

American (AMR) AF: 0.806 AC: 8442 AN: 10472

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2093 AN: 2645

East Asian (EAS) AF: 0.970 AC: 3438 AN: 3543

South Asian (SAS) AF: 0.854 AC: 2263 AN: 2650

European-Finnish (FIN) AF: 0.733 AC: 4280 AN: 5840

Middle Eastern (MID) AF: 0.758 AC: 163 AN: 215

European-Non Finnish (NFE) AF: 0.748 AC: 39617 AN: 52968

Other (OTH) AF: 0.736 AC: 1111 AN: 1510

Alfa AF: 0.714 Hom.: 10523

Bravo AF: 0.723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.040
DANN	Benign	0.25
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs5741883; hg19: chrX-12924221;