rs959060

chrX-87412105-G-AchrX-87412105-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 0.84 (27538 hom., 26913 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BS2: High Homozygotes in GnomAd at 27539 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: 0.840 AC: 92085 AN: 109602 Hom.: 27539 Cov.: 22 AF XY: 0.844 AC XY: 26856 AN XY: 31816

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.833

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.842

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: 0.840 AC: 92136 AN: 109649 Hom.: 27538 Cov.: 22 AF XY: 0.844 AC XY: 26913 AN XY: 31873

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.915

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.846

Alfa AF: 0.792 Hom.: 35626

Bravo AF: 0.849

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.27
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs959060; hg19: chrX-86667108;