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. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.682 AC: 28280 AN: 41456

American (AMR) AF: 0.383 AC: 5844 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1003 AN: 3470

East Asian (EAS) AF: 0.765 AC: 3959 AN: 5172

South Asian (SAS) AF: 0.509 AC: 2451 AN: 4814

European-Finnish (FIN) AF: 0.287 AC: 3042 AN: 10582

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.207 AC: 14073 AN: 67928

Other (OTH) AF: 0.358 AC: 754 AN: 2106

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
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs5988460; hg19: chrX-851194;