rs213443

Variant names:

• chrX-83456934-G-C
• rs213443

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 (15458 hom., 19920 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• 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=-1.05).

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: 0.607 AC: 66971 AN: 110293 Hom.: 15462 Cov.: 23

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.607

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.611

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: 0.607 AC: 66988 AN: 110345 Hom.: 15458 Cov.: 23 AF XY: 0.611 AC XY: 19920 AN XY: 32605

African (AFR) AF: 0.861 AC: 26170 AN: 30385

American (AMR) AF: 0.580 AC: 6011 AN: 10367

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1215 AN: 2630

East Asian (EAS) AF: 0.669 AC: 2314 AN: 3457

South Asian (SAS) AF: 0.476 AC: 1255 AN: 2639

European-Finnish (FIN) AF: 0.653 AC: 3764 AN: 5764

Middle Eastern (MID) AF: 0.587 AC: 125 AN: 213

European-Non Finnish (NFE) AF: 0.474 AC: 25011 AN: 52715

Other (OTH) AF: 0.605 AC: 908 AN: 1501

Alfa AF: 0.540 Hom.: 4515

Bravo AF: 0.622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.65
DANN	Benign	0.56
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs213443; hg19: chrX-82711942;