rs4827700

chrX-146265017-A-GchrX-146265017-A-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Moderate 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 0.64 (16968 hom., 20119 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BS2: High Homozygotes in GnomAd at 16978 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: 0.642 AC: 70469 AN: 109835 Hom.: 16978 Cov.: 22 AF XY: 0.626 AC XY: 20078 AN XY: 32071

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.612

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: 0.641 AC: 70486 AN: 109888 Hom.: 16968 Cov.: 22 AF XY: 0.626 AC XY: 20119 AN XY: 32136

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.608

Alfa AF: 0.566 Hom.: 29064

Bravo AF: 0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
Cadd	Benign	4.1
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4827700; hg19: chrX-145346535;