rs213443

Positions:

• chrX-83456934-G-C

Variant summary

Our verdict is Likely benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.83456934G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.607 AC: 66971 AN: 110293 Hom.: 15462 Cov.: 23 AF XY: 0.611 AC XY: 19888 AN XY: 32543

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

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.605

Alfa AF: 0.540 Hom.: 4515

Bravo AF: 0.622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs213443; hg19: chrX-82711942;