X-84961969-C-G

Variant names:

• chrX-84961969-C-G
• rs485709

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.76 (23015 hom., 24598 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.763 AC: 83764 AN: 109724 Hom.: 23016 Cov.: 22 AF XY: 0.766 AC XY: 24536 AN XY: 32032

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.774

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: 0.764 AC: 83821 AN: 109773 Hom.: 23015 Cov.: 22 AF XY: 0.767 AC XY: 24598 AN XY: 32091

Gnomad4 AFR AF: 0.922

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.851

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.772

Alfa AF: 0.712 Hom.: 5468

Bravo AF: 0.768

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs485709; hg19: chrX-84216975;