chrX-80869449-A-G

Variant names:

• chrX-80869449-A-G
• rs11266593

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 0.0909 in 111,283 control chromosomes in the GnomAD database, including 876 homozygotes. There are 2,880 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 0.091 (876 hom., 2880 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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: 0.0908 AC: 10100 AN: 111231 Hom.: 874 Cov.: 23

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.00582

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0419

Gnomad EAS AF: 0.000283

Gnomad SAS AF: 0.0107

Gnomad FIN AF: 0.0899

Gnomad MID AF: 0.0675

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0728

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

GnomAD4 genome AF: 0.0909 AC: 10118 AN: 111283 Hom.: 876 Cov.: 23 AF XY: 0.0857 AC XY: 2880 AN XY: 33589

African (AFR) AF: 0.273 AC: 8328 AN: 30545

American (AMR) AF: 0.0396 AC: 415 AN: 10483

Ashkenazi Jewish (ASJ) AF: 0.0419 AC: 110 AN: 2625

East Asian (EAS) AF: 0.000284 AC: 1 AN: 3520

South Asian (SAS) AF: 0.0111 AC: 30 AN: 2697

European-Finnish (FIN) AF: 0.0899 AC: 534 AN: 5940

Middle Eastern (MID) AF: 0.0737 AC: 16 AN: 217

European-Non Finnish (NFE) AF: 0.0108 AC: 572 AN: 53053

Other (OTH) AF: 0.0712 AC: 108 AN: 1516

Alfa AF: 0.0600 Hom.: 314

Bravo AF: 0.0963

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.57
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs11266593; hg19: chrX-80124948;