X-146334683-C-T

Variant names:

• chrX-146334683-C-T
• rs5919666

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 0.53 (11236 hom., 16999 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.533 AC: 58459 AN: 109776 Hom.: 11231 Cov.: 22 AF XY: 0.528 AC XY: 16957 AN XY: 32108

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.527

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: 0.533 AC: 58509 AN: 109827 Hom.: 11236 Cov.: 22 AF XY: 0.528 AC XY: 16999 AN XY: 32169

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.527

Alfa AF: 0.479 Hom.: 10854

Bravo AF: 0.541

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5919666; hg19: chrX-145416201;