rs2202091

Variant names:

• chrX-146004438-C-A
• rs2202091

Your query was ambiguous. Multiple possible variants found:

• chrX-146004438-C-A
• chrX-146004438-C-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 0.60 (14349 hom., 17793 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

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: 0.599 AC: 64367 AN: 107420 Hom.: 14338 Cov.: 21

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.572

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: 0.599 AC: 64413 AN: 107463 Hom.: 14349 Cov.: 21 AF XY: 0.593 AC XY: 17793 AN XY: 29991

African (AFR) AF: 0.737 AC: 21769 AN: 29544

American (AMR) AF: 0.554 AC: 5483 AN: 9903

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1137 AN: 2603

East Asian (EAS) AF: 0.590 AC: 1985 AN: 3362

South Asian (SAS) AF: 0.637 AC: 1537 AN: 2413

European-Finnish (FIN) AF: 0.551 AC: 2893 AN: 5246

Middle Eastern (MID) AF: 0.588 AC: 124 AN: 211

European-Non Finnish (NFE) AF: 0.545 AC: 28372 AN: 52064

Other (OTH) AF: 0.575 AC: 839 AN: 1460

Alfa AF: 0.577 Hom.: 4341

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.36
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2202091; hg19: chrX-145085956;