rs223678

Variant names:

• chrX-89582521-G-A
• rs223678

Your query was ambiguous. Multiple possible variants found:

• chrX-89582521-G-A
• chrX-89582521-G-C
• chrX-89582521-G-T

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 0.72 (20997 hom., 7581 hem., cov: 13)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• 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=-0.97).

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: 0.723 AC: 61412 AN: 84988 Hom.: 21004 Cov.: 13

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.721

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: AS_VQSR;InbreedingCoeff AF: 0.722 AC: 61424 AN: 85023 Hom.: 20997 Cov.: 13 AF XY: 0.501 AC XY: 7581 AN XY: 15117

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.641 AC: 14847 AN: 23157

American (AMR) AF: 0.654 AC: 4845 AN: 7410

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 1659 AN: 2158

East Asian (EAS) AF: 0.654 AC: 1725 AN: 2639

South Asian (SAS) AF: 0.459 AC: 779 AN: 1696

European-Finnish (FIN) AF: 0.691 AC: 2416 AN: 3495

Middle Eastern (MID) AF: 0.811 AC: 133 AN: 164

European-Non Finnish (NFE) AF: 0.793 AC: 33830 AN: 42677

Other (OTH) AF: 0.722 AC: 785 AN: 1088

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.796 Hom.: 5839

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.78
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs223678; hg19: chrX-88837520;