chrX-121839996-A-G

Variant names:

• chrX-121839996-A-G
• rs4509467

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 0.75 (22274 hom., 24679 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.749 AC: 82751 AN: 110488 Hom.: 22281 Cov.: 23

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.584

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.707

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: 0.749 AC: 82788 AN: 110539 Hom.: 22274 Cov.: 23 AF XY: 0.752 AC XY: 24679 AN XY: 32803

African (AFR) AF: 0.899 AC: 27413 AN: 30506

American (AMR) AF: 0.778 AC: 8047 AN: 10347

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1470 AN: 2619

East Asian (EAS) AF: 0.969 AC: 3406 AN: 3514

South Asian (SAS) AF: 0.683 AC: 1822 AN: 2667

European-Finnish (FIN) AF: 0.729 AC: 4235 AN: 5812

Middle Eastern (MID) AF: 0.575 AC: 122 AN: 212

European-Non Finnish (NFE) AF: 0.660 AC: 34796 AN: 52703

Other (OTH) AF: 0.701 AC: 1041 AN: 1485

Alfa AF: 0.590 Hom.: 4166

Bravo AF: 0.763

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.40
DANN	Benign	0.29
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs4509467; hg19: chrX-120973849;