rs1041668

chrX-66866114-G-AchrX-66866114-G-CchrX-66866114-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 0.65 (20514 hom., 21885 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS2: High Homozygotes in GnomAd at 20522 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: 0.655 AC: 72394 AN: 110591 Hom.: 20522 Cov.: 23 AF XY: 0.666 AC XY: 21873 AN XY: 32829

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.754

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.707

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: 0.654 AC: 72384 AN: 110644 Hom.: 20514 Cov.: 23 AF XY: 0.665 AC XY: 21885 AN XY: 32892

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.928

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.846

Gnomad4 OTH AF: 0.710

Alfa AF: 0.818 Hom.: 28950

Bravo AF: 0.637

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.60
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1041668; hg19: chrX-66085956; COSMIC: COSV68315964;