rs5946512

Positions:

• chrX-857367-A-G
• chrX-857367-A-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 0.436 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66053 AN: 151730 Hom.: 15722 Cov.: 31 AF XY: 0.438 AC XY: 32406 AN XY: 74030

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

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.401

Bravo AF: 0.448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946512; hg19: chrX-818102;