rs5988284

Variant names:

• chrX-857241-G-A
• rs5988284

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 0.284 in 151,980 control chromosomes in the GnomAD database, including 6,310 homozygotes. There are 20,881 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 0.28 (6310 hom., 20881 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

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 (SAS) allele frequency at 95% confidence interval = 0.297 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: 0.284 AC: 43074 AN: 151862 Hom.: 6309 Cov.: 32 AF XY: 0.281 AC XY: 20856 AN XY: 74142

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.284 AC: 43094 AN: 151980 Hom.: 6310 Cov.: 32 AF XY: 0.281 AC XY: 20881 AN XY: 74270

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.279

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5988284; hg19: chrX-817976;