chrX-28214936-G-A

Position:

• chrX-28214936-G-A

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 0.77 (22925 hom., 25316 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.767 AC: 84813 AN: 110562 Hom.: 22919 Cov.: 23 AF XY: 0.770 AC XY: 25252 AN XY: 32774

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.676

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.759

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: 0.767 AC: 84879 AN: 110615 Hom.: 22925 Cov.: 23 AF XY: 0.771 AC XY: 25316 AN XY: 32837

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.762

Alfa AF: 0.733 Hom.: 72944

Bravo AF: 0.778

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.059
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5971305; hg19: chrX-28233053;