rs6525481

chrX-71209374-C-G

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 0.59 (14933 hom., 19391 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS2: High Homozygotes in GnomAd at 14924 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: 0.594 AC: 65652 AN: 110482 Hom.: 14924 Cov.: 23 AF XY: 0.591 AC XY: 19336 AN XY: 32742

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.660

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.618

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: 0.595 AC: 65715 AN: 110536 Hom.: 14933 Cov.: 23 AF XY: 0.591 AC XY: 19391 AN XY: 32808

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.624

Alfa AF: 0.541 Hom.: 4070

Bravo AF: 0.622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.84
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6525481; hg19: chrX-70429224;