rs5988460

Variant names:

• chrX-890459-A-G
• rs5988460

Your query was ambiguous. Multiple possible variants found:

• chrX-890459-A-G
• chrX-890459-A-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 0.394 in 151,986 control chromosomes in the GnomAD database, including 15,310 homozygotes. There are 29,819 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 0.39 (15310 hom., 29819 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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: 0.394 AC: 59794 AN: 151868 Hom.: 15272 Cov.: 32 AF XY: 0.401 AC XY: 29715 AN XY: 74152

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.394 AC: 59883 AN: 151986 Hom.: 15310 Cov.: 32 AF XY: 0.401 AC XY: 29819 AN XY: 74280

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.358

Bravo AF: 0.417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.094
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5988460; hg19: chrX-851194;