chrX-90549128-A-G

Variant names:

• chrX-90549128-A-G
• rs2755459

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 0.71 (20011 hom., 20942 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• 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=-1.03).

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: 0.709 AC: 76187 AN: 107520 Hom.: 20025 Cov.: 20

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.726

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: 0.708 AC: 76193 AN: 107572 Hom.: 20011 Cov.: 20 AF XY: 0.694 AC XY: 20942 AN XY: 30186

African (AFR) AF: 0.557 AC: 16638 AN: 29851

American (AMR) AF: 0.801 AC: 7999 AN: 9988

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2144 AN: 2583

East Asian (EAS) AF: 0.740 AC: 2494 AN: 3369

South Asian (SAS) AF: 0.646 AC: 1574 AN: 2438

European-Finnish (FIN) AF: 0.737 AC: 3894 AN: 5282

Middle Eastern (MID) AF: 0.788 AC: 171 AN: 217

European-Non Finnish (NFE) AF: 0.766 AC: 39627 AN: 51737

Other (OTH) AF: 0.719 AC: 1035 AN: 1439

Alfa AF: 0.742 Hom.: 6051

Bravo AF: 0.713

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.28
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2755459; hg19: chrX-89804127;