X-69585474-A-G

Variant names:

• chrX-69585474-A-G
• rs4844096

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 0.69 (19852 hom., 22024 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

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: 0.689 AC: 75689 AN: 109927 Hom.: 19843 Cov.: 22

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.653

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: 0.689 AC: 75753 AN: 109971 Hom.: 19852 Cov.: 22 AF XY: 0.683 AC XY: 22024 AN XY: 32247

African (AFR) AF: 0.926 AC: 27966 AN: 30198

American (AMR) AF: 0.714 AC: 7390 AN: 10343

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1298 AN: 2626

East Asian (EAS) AF: 0.997 AC: 3503 AN: 3513

South Asian (SAS) AF: 0.735 AC: 1851 AN: 2517

European-Finnish (FIN) AF: 0.553 AC: 3158 AN: 5713

Middle Eastern (MID) AF: 0.451 AC: 96 AN: 213

European-Non Finnish (NFE) AF: 0.551 AC: 29048 AN: 52677

Other (OTH) AF: 0.658 AC: 987 AN: 1501

Alfa AF: 0.606 Hom.: 65350

Bravo AF: 0.714

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.66
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4844096; hg19: chrX-68805318;