rs381365

Positions:

• chrX-146667390-T-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 0.86 (28961 hom., 27455 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

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: 0.856 AC: 94158 AN: 110000 Hom.: 28969 Cov.: 22 AF XY: 0.850 AC XY: 27404 AN XY: 32256

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.853

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: 0.856 AC: 94193 AN: 110050 Hom.: 28961 Cov.: 22 AF XY: 0.850 AC XY: 27455 AN XY: 32316

Gnomad4 AFR AF: 0.972

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.844

Alfa AF: 0.828 Hom.: 86371

Bravo AF: 0.859

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
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: rs381365; hg19: chrX-145748908;