X-127221560-G-T

Position:

• chrX-127221560-G-T

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 0.289 in 109,818 control chromosomes in the GnomAD database, including 3,725 homozygotes. There are 9,125 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 0.29 (3725 hom., 9125 hem., cov: 22)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.127221560G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.289 AC: 31686 AN: 109767 Hom.: 3726 Cov.: 22 AF XY: 0.284 AC XY: 9113 AN XY: 32087

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.289 AC: 31699 AN: 109818 Hom.: 3725 Cov.: 22 AF XY: 0.284 AC XY: 9125 AN XY: 32148

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.283

Alfa AF: 0.118 Hom.: 555

Bravo AF: 0.307

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs275978; hg19: chrX-126355543;