rs3125945

chrX-71038886-A-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 0.63 (16615 hom., 20208 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd at 16609 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: 0.632 AC: 69705 AN: 110347 Hom.: 16609 Cov.: 22 AF XY: 0.619 AC XY: 20161 AN XY: 32585

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.636

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: 0.632 AC: 69755 AN: 110398 Hom.: 16615 Cov.: 22 AF XY: 0.619 AC XY: 20208 AN XY: 32646

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.642

Alfa AF: 0.566 Hom.: 37705

Bravo AF: 0.656

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.28
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3125945; hg19: chrX-70258736;