X-866590-G-A

Variant names:

• chrX-866590-G-A
• rs5946518

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 0.331 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
• 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 (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

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

African (AFR) AF: 0.388 AC: 16101 AN: 41462

American (AMR) AF: 0.358 AC: 5461 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2192 AN: 5154

South Asian (SAS) AF: 0.305 AC: 1468 AN: 4812

European-Finnish (FIN) AF: 0.271 AC: 2861 AN: 10538

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20189 AN: 67938

Other (OTH) AF: 0.328 AC: 692 AN: 2110

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
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs5946518; hg19: chrX-827325;