rs12559781

chrX-4297911-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.53 (11921 hom., 16690 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BS2: High Homozygotes in GnomAd at 11917 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.531 AC: 58583 AN: 110308 Hom.: 11917 Cov.: 22 AF XY: 0.509 AC XY: 16635 AN XY: 32656

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.530

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.519

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: 0.531 AC: 58627 AN: 110364 Hom.: 11921 Cov.: 22 AF XY: 0.510 AC XY: 16690 AN XY: 32722

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.512

Alfa AF: 0.498 Hom.: 17840

Bravo AF: 0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.52
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12559781; hg19: chrX-4215952;