chrX-83280161-G-A

Position:

• chrX-83280161-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 0.196 in 110,614 control chromosomes in the GnomAD database, including 1,681 homozygotes. There are 6,295 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 0.20 (1681 hom., 6295 hem., cov: 22)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.83280161G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.196 AC: 21651 AN: 110563 Hom.: 1681 Cov.: 22 AF XY: 0.191 AC XY: 6285 AN XY: 32883

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0381

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.196 AC: 21657 AN: 110614 Hom.: 1681 Cov.: 22 AF XY: 0.191 AC XY: 6295 AN XY: 32944

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.219

Alfa AF: 0.126 Hom.: 1715

Bravo AF: 0.213

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0010
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1410530; hg19: chrX-82535169;