X-78327951-C-T

Variant names:

• chrX-78327951-C-T
• rs2806489

Variant summary

Our verdict is Likely benign. The variant received -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 0.79 (24654 hom., 25779 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 8 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.787 AC: 87218 AN: 110841 Hom.: 24660 Cov.: 23

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.757

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: 0.787 AC: 87261 AN: 110899 Hom.: 24654 Cov.: 23 AF XY: 0.778 AC XY: 25779 AN XY: 33121

African (AFR) AF: 0.904 AC: 27608 AN: 30545

American (AMR) AF: 0.671 AC: 7013 AN: 10447

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2158 AN: 2647

East Asian (EAS) AF: 0.594 AC: 2085 AN: 3509

South Asian (SAS) AF: 0.621 AC: 1638 AN: 2637

European-Finnish (FIN) AF: 0.777 AC: 4530 AN: 5829

Middle Eastern (MID) AF: 0.765 AC: 166 AN: 217

European-Non Finnish (NFE) AF: 0.765 AC: 40483 AN: 52890

Other (OTH) AF: 0.753 AC: 1136 AN: 1508

Alfa AF: 0.793 Hom.: 27492

Bravo AF: 0.784

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.49
DANN	Benign	0.76
PhyloP100		0.022
PromoterAI		0.015	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2806489; hg19: chrX-77583448;