rs5907577

Variant names:

• chrX-140084524-C-T
• rs5907577

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 0.246 in 111,201 control chromosomes in the GnomAD database, including 2,743 homozygotes. There are 8,283 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 0.25 (2743 hom., 8283 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.768

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.428 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: 0.246 AC: 27365 AN: 111146 Hom.: 2747 Cov.: 23 AF XY: 0.248 AC XY: 8281 AN XY: 33366

Gnomad AFR AF: 0.0983

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.246 AC: 27350 AN: 111201 Hom.: 2743 Cov.: 23 AF XY: 0.248 AC XY: 8283 AN XY: 33431

Gnomad4 AFR AF: 0.0982

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.247

Alfa AF: 0.255 Hom.: 1997

Bravo AF: 0.233

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5907577; hg19: chrX-139166683;