rs5988284

Positions:

• chrX-857241-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;