rs7884258

chrX-71204813-C-AchrX-71204813-C-GchrX-71204813-C-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 0.60 (14973 hom., 17430 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.16

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BS2: High Homozygotes in GnomAd at 14963 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: 0.597 AC: 63682 AN: 106758 Hom.: 14963 Cov.: 20 AF XY: 0.592 AC XY: 17377 AN XY: 29366

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.681

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.626

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: 0.597 AC: 63744 AN: 106811 Hom.: 14973 Cov.: 20 AF XY: 0.592 AC XY: 17430 AN XY: 29429

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.633

Alfa AF: 0.294 Hom.: 1170

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.12
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7884258; hg19: chrX-70424663;