rs4301558

Variant names:

• chrX-43652206-C-A
• rs4301558

Your query was ambiguous. Multiple possible variants found:

• chrX-43652206-C-A
• chrX-43652206-C-G
• chrX-43652206-C-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 0.69 (19098 hom., 22132 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• 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=-0.94).

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: 0.690 AC: 76299 AN: 110579 Hom.: 19096 Cov.: 23

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.698

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.690

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: 0.690 AC: 76341 AN: 110632 Hom.: 19098 Cov.: 23 AF XY: 0.673 AC XY: 22132 AN XY: 32900

African (AFR) AF: 0.741 AC: 22475 AN: 30315

American (AMR) AF: 0.696 AC: 7235 AN: 10394

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 1828 AN: 2645

East Asian (EAS) AF: 0.420 AC: 1455 AN: 3463

South Asian (SAS) AF: 0.385 AC: 1013 AN: 2629

European-Finnish (FIN) AF: 0.566 AC: 3336 AN: 5897

Middle Eastern (MID) AF: 0.706 AC: 151 AN: 214

European-Non Finnish (NFE) AF: 0.706 AC: 37353 AN: 52876

Other (OTH) AF: 0.686 AC: 1046 AN: 1524

Alfa AF: 0.696 Hom.: 5543

Bravo AF: 0.702

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.50
DANN	Benign	0.67
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4301558;

hg19: chrX-43511454;