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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs4301558; hg19: chrX-43511454;