X-84708918-G-A

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).

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: 0.838 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 v4.3

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;