rs5919324

Variant names:

• chrX-67210798-G-A
• rs5919324

Your query was ambiguous. Multiple possible variants found:

• chrX-67210798-G-A
• chrX-67210798-G-C

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 0.65 (20380 hom., 21350 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994
• 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=-0.65).

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: 0.652 AC: 71694 AN: 109901 Hom.: 20390 Cov.: 22

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.760

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.695

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: 0.652 AC: 71680 AN: 109954 Hom.: 20380 Cov.: 22 AF XY: 0.662 AC XY: 21350 AN XY: 32236

African (AFR) AF: 0.138 AC: 4191 AN: 30445

American (AMR) AF: 0.828 AC: 8441 AN: 10195

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 2413 AN: 2627

East Asian (EAS) AF: 0.998 AC: 3465 AN: 3471

South Asian (SAS) AF: 0.917 AC: 2336 AN: 2548

European-Finnish (FIN) AF: 0.829 AC: 4686 AN: 5656

Middle Eastern (MID) AF: 0.756 AC: 161 AN: 213

European-Non Finnish (NFE) AF: 0.843 AC: 44356 AN: 52646

Other (OTH) AF: 0.697 AC: 1031 AN: 1479

Alfa AF: 0.814 Hom.: 23663

Bravo AF: 0.635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.1
DANN	Benign	0.61
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs5919324; hg19: chrX-66430640;