rs5946518

Variant names:

• chrX-866590-G-A
• rs5946518

Your query was ambiguous. Multiple possible variants found:

• chrX-866590-G-A
• chrX-866590-G-T

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 0.331 in 151,936 control chromosomes in the GnomAD database, including 8,654 homozygotes. There are 24,557 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 0.33 (8654 hom., 24557 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 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: 0.330 AC: 50166 AN: 151818 Hom.: 8640 Cov.: 32 AF XY: 0.331 AC XY: 24509 AN XY: 74094

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.331 AC: 50215 AN: 151936 Hom.: 8654 Cov.: 32 AF XY: 0.331 AC XY: 24557 AN XY: 74222

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.328

Bravo AF: 0.340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946518; hg19: chrX-827325;