rs2221799

Variant names:

• chrX-67156774-G-A
• rs2221799

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 0.65 (20383 hom., 21704 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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: 0.653 AC: 72040 AN: 110358 Hom.: 20393 Cov.: 23

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.702

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: 0.652 AC: 72025 AN: 110410 Hom.: 20383 Cov.: 23 AF XY: 0.664 AC XY: 21704 AN XY: 32678

African (AFR) AF: 0.138 AC: 4200 AN: 30543

American (AMR) AF: 0.827 AC: 8488 AN: 10268

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 2418 AN: 2632

East Asian (EAS) AF: 0.998 AC: 3476 AN: 3482

South Asian (SAS) AF: 0.919 AC: 2343 AN: 2550

European-Finnish (FIN) AF: 0.829 AC: 4743 AN: 5721

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

European-Non Finnish (NFE) AF: 0.843 AC: 44535 AN: 52818

Other (OTH) AF: 0.704 AC: 1059 AN: 1505

Alfa AF: 0.821 Hom.: 44000

Bravo AF: 0.635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.30
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2221799; hg19: chrX-66376616;