rs6623084

Variant names:

• chrX-84708918-G-A
• rs6623084

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 0.84 (27262 hom., 25163 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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: 0.838 AC: 89993 AN: 107437 Hom.: 27274 Cov.: 20

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.904

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.881

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: 0.837 AC: 89991 AN: 107455 Hom.: 27262 Cov.: 20 AF XY: 0.841 AC XY: 25163 AN XY: 29921

African (AFR) AF: 0.745 AC: 22041 AN: 29576

American (AMR) AF: 0.922 AC: 9113 AN: 9881

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 2376 AN: 2614

East Asian (EAS) AF: 0.985 AC: 3317 AN: 3367

South Asian (SAS) AF: 0.882 AC: 2145 AN: 2432

European-Finnish (FIN) AF: 0.872 AC: 4351 AN: 4988

Middle Eastern (MID) AF: 0.895 AC: 187 AN: 209

European-Non Finnish (NFE) AF: 0.855 AC: 44683 AN: 52270

Other (OTH) AF: 0.879 AC: 1274 AN: 1450

Alfa AF: 0.844 Hom.: 43163

Bravo AF: 0.840

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.62
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs6623084; hg19: chrX-83963926;