rs4827700

Variant names:

• chrX-146265017-A-G
• rs4827700

Your query was ambiguous. Multiple possible variants found:

• chrX-146265017-A-G
• chrX-146265017-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

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 (16968 hom., 20119 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 1 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).

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: 0.642 AC: 70469 AN: 109835 Hom.: 16978 Cov.: 22

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.612

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: 0.641 AC: 70486 AN: 109888 Hom.: 16968 Cov.: 22 AF XY: 0.626 AC XY: 20119 AN XY: 32136

African (AFR) AF: 0.826 AC: 24916 AN: 30173

American (AMR) AF: 0.472 AC: 4861 AN: 10294

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1504 AN: 2619

East Asian (EAS) AF: 0.692 AC: 2362 AN: 3415

South Asian (SAS) AF: 0.579 AC: 1475 AN: 2546

European-Finnish (FIN) AF: 0.531 AC: 3044 AN: 5732

Middle Eastern (MID) AF: 0.561 AC: 119 AN: 212

European-Non Finnish (NFE) AF: 0.588 AC: 30979 AN: 52712

Other (OTH) AF: 0.608 AC: 917 AN: 1509

Alfa AF: 0.587 Hom.: 48093

Bravo AF: 0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	4.1
DANN	Benign	0.70
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs4827700; hg19: chrX-145346535;