chrX-866815-T-G

Variant names:

• chrX-866815-T-G
• rs5946520

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 0.447 in 151,502 control chromosomes in the GnomAD database, including 15,803 homozygotes. There are 32,536 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 0.45 (15803 hom., 32536 hem., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 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: 0.447 AC: 67598 AN: 151386 Hom.: 15762 Cov.: 29

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.447 AC: 67694 AN: 151502 Hom.: 15803 Cov.: 29 AF XY: 0.440 AC XY: 32536 AN XY: 73970

African (AFR) AF: 0.569 AC: 23513 AN: 41310

American (AMR) AF: 0.425 AC: 6459 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3462

East Asian (EAS) AF: 0.455 AC: 2328 AN: 5114

South Asian (SAS) AF: 0.377 AC: 1808 AN: 4802

European-Finnish (FIN) AF: 0.308 AC: 3229 AN: 10494

Middle Eastern (MID) AF: 0.344 AC: 99 AN: 288

European-Non Finnish (NFE) AF: 0.412 AC: 27969 AN: 67848

Other (OTH) AF: 0.441 AC: 922 AN: 2092

Bravo AF: 0.463

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.041
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs5946520; hg19: chrX-827550;