X-30313232-A-G

Position:

• chrX-30313232-A-G

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 0.80 (25369 hom., 26290 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).

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: 0.802 AC: 88659 AN: 110580 Hom.: 25376 Cov.: 23 AF XY: 0.801 AC XY: 26251 AN XY: 32792

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.833

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.813

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: 0.802 AC: 88680 AN: 110634 Hom.: 25369 Cov.: 23 AF XY: 0.800 AC XY: 26290 AN XY: 32856

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.807

Alfa AF: 0.855 Hom.: 104864

Bravo AF: 0.784

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.9
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1034948; hg19: chrX-30331349;