rs1926025

chrX-46359554-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong 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 0.91 (32369 hom., 29533 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS2: High Homozygotes in GnomAd at 32380 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: 0.908 AC: 99999 AN: 110153 Hom.: 32380 Cov.: 22 AF XY: 0.911 AC XY: 29490 AN XY: 32375

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.918

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: 0.908 AC: 100025 AN: 110201 Hom.: 32369 Cov.: 22 AF XY: 0.911 AC XY: 29533 AN XY: 32433

Gnomad4 AFR AF: 0.749

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.986

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.938

Gnomad4 FIN AF: 0.988

Gnomad4 NFE AF: 0.984

Gnomad4 OTH AF: 0.919

Alfa AF: 0.935 Hom.: 10399

Bravo AF: 0.891

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.18
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1926025; hg19: chrX-46218989;