rs5946512

Variant names:

• chrX-857367-A-G
• rs5946512

Your query was ambiguous. Multiple possible variants found:

• chrX-857367-A-G
• chrX-857367-A-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 0.436 in 151,848 control chromosomes in the GnomAD database, including 15,757 homozygotes. There are 32,493 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 0.44 (15757 hom., 32493 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66053 AN: 151730 Hom.: 15722 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.436 AC: 66150 AN: 151848 Hom.: 15757 Cov.: 31 AF XY: 0.438 AC XY: 32493 AN XY: 74158

African (AFR) AF: 0.593 AC: 24561 AN: 41422

American (AMR) AF: 0.425 AC: 6468 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3468

East Asian (EAS) AF: 0.697 AC: 3593 AN: 5152

South Asian (SAS) AF: 0.501 AC: 2409 AN: 4810

European-Finnish (FIN) AF: 0.349 AC: 3686 AN: 10564

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23257 AN: 67898

Other (OTH) AF: 0.401 AC: 844 AN: 2104

Bravo AF: 0.448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.4
DANN	Benign	0.20
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs5946512; hg19: chrX-818102;