X-80869449-A-G

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 0.0909 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0908 AC: 10100 AN: 111231 Hom.: 874 Cov.: 23 AF XY: 0.0855 AC XY: 2867 AN XY: 33527

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

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.0396

Gnomad4 ASJ AF: 0.0419

Gnomad4 EAS AF: 0.000284

Gnomad4 SAS AF: 0.0111

Gnomad4 FIN AF: 0.0899

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.0712

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11266593; hg19: chrX-80124948;