chrX-853599-G-A

Position:

• chrX-853599-G-A

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 0.443 in 151,736 control chromosomes in the GnomAD database, including 15,169 homozygotes. There are 32,910 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 0.44 (15169 hom., 32910 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 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: 0.443 AC: 67171 AN: 151618 Hom.: 15143 Cov.: 31 AF XY: 0.444 AC XY: 32853 AN XY: 73958

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.443 AC: 67230 AN: 151736 Hom.: 15169 Cov.: 31 AF XY: 0.444 AC XY: 32910 AN XY: 74086

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.491

Bravo AF: 0.452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5946326; hg19: chrX-814334;