rs10521884

chrX-149461305-G-AchrX-149461305-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 0.81 (27364 hom., 26199 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

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 27374 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: 0.809 AC: 88925 AN: 109927 Hom.: 27374 Cov.: 22 AF XY: 0.813 AC XY: 26178 AN XY: 32181

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.986

Gnomad MID AF: 0.945

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.814

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: 0.809 AC: 88925 AN: 109977 Hom.: 27364 Cov.: 22 AF XY: 0.813 AC XY: 26199 AN XY: 32241

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.995

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.986

Gnomad4 NFE AF: 0.981

Gnomad4 OTH AF: 0.816

Alfa AF: 0.876 Hom.: 7359

Bravo AF: 0.771

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.66
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521884; hg19: chrX-148542836;