rs1293470

Variant names:

• chrX-123078079-A-G
• rs1293470

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 (19054 hom., 22372 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

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: 0.686 AC: 76023 AN: 110895 Hom.: 19056 Cov.: 24

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.702

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: 0.686 AC: 76058 AN: 110948 Hom.: 19054 Cov.: 24 AF XY: 0.673 AC XY: 22372 AN XY: 33242

African (AFR) AF: 0.733 AC: 22413 AN: 30576

American (AMR) AF: 0.534 AC: 5557 AN: 10397

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2083 AN: 2632

East Asian (EAS) AF: 0.228 AC: 802 AN: 3513

South Asian (SAS) AF: 0.390 AC: 1050 AN: 2690

European-Finnish (FIN) AF: 0.678 AC: 4017 AN: 5924

Middle Eastern (MID) AF: 0.745 AC: 158 AN: 212

European-Non Finnish (NFE) AF: 0.726 AC: 38367 AN: 52814

Other (OTH) AF: 0.702 AC: 1062 AN: 1512

Alfa AF: 0.691 Hom.: 28895

Bravo AF: 0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.0
DANN	Benign	0.78
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1293470; hg19: chrX-122211932;