chrX-33627573-G-A

Position:

• chrX-33627573-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 0.375 in 110,832 control chromosomes in the GnomAD database, including 6,567 homozygotes. There are 12,418 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 0.38 (6567 hom., 12418 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.33627573G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.375 AC: 41597 AN: 110780 Hom.: 6569 Cov.: 23 AF XY: 0.375 AC XY: 12416 AN XY: 33070

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.00678

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.375 AC: 41585 AN: 110832 Hom.: 6567 Cov.: 23 AF XY: 0.375 AC XY: 12418 AN XY: 33132

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.00708

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.386

Alfa AF: 0.467 Hom.: 29663

Bravo AF: 0.353

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.031
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1518519; hg19: chrX-33645690;