rs4557887

Variant names:

• chrX-25717311-G-A
• rs4557887

Your query was ambiguous. Multiple possible variants found:

• chrX-25717311-G-A
• chrX-25717311-G-C
• chrX-25717311-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.429 in 111,093 control chromosomes in the GnomAD database, including 7,455 homozygotes. There are 14,205 hemizygotes in GnomAD. 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 0.43 (7455 hom., 14205 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

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: 0.429 AC: 47596 AN: 111040 Hom.: 7457 Cov.: 23 AF XY: 0.426 AC XY: 14180 AN XY: 33290

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.0917

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.419

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.429 AC: 47617 AN: 111093 Hom.: 7455 Cov.: 23 AF XY: 0.426 AC XY: 14205 AN XY: 33353

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.422

Alfa AF: 0.395 Hom.: 3106

Bravo AF: 0.444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.93
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4557887; hg19: chrX-25735428;