rs5946759

Variant names:

• chrX-745556-G-A
• rs5946759

Your query was ambiguous. Multiple possible variants found:

• chrX-745556-G-A
• chrX-745556-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 0.0665 in 152,184 control chromosomes in the GnomAD database, including 484 homozygotes. There are 4,795 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 0.067 (484 hom., 4795 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

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 (NFE) allele frequency at 95% confidence interval = 0.0972 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: 0.0665 AC: 10114 AN: 152066 Hom.: 483 Cov.: 32 AF XY: 0.0644 AC XY: 4784 AN XY: 74252

Gnomad AFR AF: 0.0215

Gnomad AMI AF: 0.0518

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.00808

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0992

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0665 AC: 10122 AN: 152184 Hom.: 484 Cov.: 32 AF XY: 0.0645 AC XY: 4795 AN XY: 74380

Gnomad4 AFR AF: 0.0217

Gnomad4 AMR AF: 0.0552

Gnomad4 ASJ AF: 0.0464

Gnomad4 EAS AF: 0.00791

Gnomad4 SAS AF: 0.0513

Gnomad4 FIN AF: 0.0951

Gnomad4 NFE AF: 0.0992

Gnomad4 OTH AF: 0.0563

Bravo AF: 0.0589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946759; hg19: chrX-706291;