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. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.0217 AC: 903 AN: 41542

American (AMR) AF: 0.0552 AC: 845 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 161 AN: 3470

East Asian (EAS) AF: 0.00791 AC: 41 AN: 5184

South Asian (SAS) AF: 0.0513 AC: 247 AN: 4812

European-Finnish (FIN) AF: 0.0951 AC: 1006 AN: 10576

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0992 AC: 6744 AN: 67982

Other (OTH) AF: 0.0563 AC: 119 AN: 2114

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs5946759; hg19: chrX-706291;