rs1402076

Variant names:

• chrX-93266680-A-G
• rs1402076

Your query was ambiguous. Multiple possible variants found:

• chrX-93266680-A-G
• chrX-93266680-A-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 0.64 (16434 hom., 20370 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• 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=-0.95).

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: 0.636 AC: 69949 AN: 109937 Hom.: 16428 Cov.: 22

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.502

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.615

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: 0.636 AC: 69998 AN: 109982 Hom.: 16434 Cov.: 22 AF XY: 0.631 AC XY: 20370 AN XY: 32282

African (AFR) AF: 0.804 AC: 24366 AN: 30303

American (AMR) AF: 0.662 AC: 6827 AN: 10319

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 1583 AN: 2612

East Asian (EAS) AF: 0.627 AC: 2155 AN: 3435

South Asian (SAS) AF: 0.768 AC: 2001 AN: 2607

European-Finnish (FIN) AF: 0.465 AC: 2687 AN: 5773

Middle Eastern (MID) AF: 0.509 AC: 111 AN: 218

European-Non Finnish (NFE) AF: 0.548 AC: 28824 AN: 52551

Other (OTH) AF: 0.621 AC: 924 AN: 1488

Alfa AF: 0.585 Hom.: 4224

Bravo AF: 0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.44
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1402076; hg19: chrX-92521679;