chrX-83336462-A-G

Variant names:

• chrX-83336462-A-G
• rs1299087

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

ACMG classification

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Publications

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Other links and lift over

dbSNP: rs1299087; hg19: chrX-82591470;