X-33618320-A-G

Position:

• chrX-33618320-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 0.118 in 111,016 control chromosomes in the GnomAD database, including 1,198 homozygotes. There are 3,848 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 0.12 (1198 hom., 3848 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.118 AC: 13106 AN: 110962 Hom.: 1199 Cov.: 23 AF XY: 0.115 AC XY: 3833 AN XY: 33314

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0299

Gnomad MID AF: 0.0664

Gnomad NFE AF: 0.0103

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.118 AC: 13125 AN: 111016 Hom.: 1198 Cov.: 23 AF XY: 0.115 AC XY: 3848 AN XY: 33378

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.0282

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0299

Gnomad4 NFE AF: 0.0103

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0760 Hom.: 414

Bravo AF: 0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.055
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs961747; hg19: chrX-33636437;