rs1299087

Variant names:

• chrX-83336462-A-G
• rs1299087

Your query was ambiguous. Multiple possible variants found:

• chrX-83336462-A-G
• chrX-83336462-A-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.61 (15621 hom., 19808 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03
• Publications: 2 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.613 AC: 67214 AN: 109689 Hom.: 15624 Cov.: 22

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.626

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.607

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.613 AC: 67233 AN: 109736 Hom.: 15621 Cov.: 22 AF XY: 0.615 AC XY: 19808 AN XY: 32190

African (AFR) AF: 0.863 AC: 26172 AN: 30337

American (AMR) AF: 0.583 AC: 5970 AN: 10244

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1207 AN: 2623

East Asian (EAS) AF: 0.562 AC: 1937 AN: 3447

South Asian (SAS) AF: 0.472 AC: 1239 AN: 2627

European-Finnish (FIN) AF: 0.665 AC: 3803 AN: 5719

Middle Eastern (MID) AF: 0.608 AC: 132 AN: 217

European-Non Finnish (NFE) AF: 0.490 AC: 25654 AN: 52346

Other (OTH) AF: 0.601 AC: 901 AN: 1498

Alfa AF: 0.568 Hom.: 5725

Bravo AF: 0.623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.66
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs1299087; hg19: chrX-82591470;