rs2213481

Variant names:

• chrX-76066365-G-A
• rs2213481

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 0.74 (22669 hom., 23550 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.742 AC: 81854 AN: 110339 Hom.: 22673 Cov.: 23

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.760

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: 0.742 AC: 81892 AN: 110391 Hom.: 22669 Cov.: 23 AF XY: 0.721 AC XY: 23550 AN XY: 32641

African (AFR) AF: 0.851 AC: 25872 AN: 30406

American (AMR) AF: 0.606 AC: 6236 AN: 10282

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2207 AN: 2630

East Asian (EAS) AF: 0.120 AC: 418 AN: 3496

South Asian (SAS) AF: 0.464 AC: 1216 AN: 2620

European-Finnish (FIN) AF: 0.664 AC: 3832 AN: 5767

Middle Eastern (MID) AF: 0.816 AC: 173 AN: 212

European-Non Finnish (NFE) AF: 0.762 AC: 40249 AN: 52804

Other (OTH) AF: 0.758 AC: 1133 AN: 1494

Alfa AF: 0.742 Hom.: 24718

Bravo AF: 0.740

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.27
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs2213481; hg19: chrX-75286200;