rs5908574

Variant names:

• chrX-143166387-G-A
• rs5908574

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 0.385 in 110,345 control chromosomes in the GnomAD database, including 7,403 homozygotes. There are 12,248 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 0.38 (7403 hom., 12248 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 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: 0.384 AC: 42405 AN: 110293 Hom.: 7401 Cov.: 23 AF XY: 0.374 AC XY: 12208 AN XY: 32611

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.385 AC: 42448 AN: 110345 Hom.: 7403 Cov.: 23 AF XY: 0.375 AC XY: 12248 AN XY: 32673

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.359

Alfa AF: 0.279 Hom.: 21608

Bravo AF: 0.390

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5908574; hg19: chrX-142254173;