chrX-25717311-G-A

Position:

• chrX-25717311-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 0.429 in 111,093 control chromosomes in the GnomAD database, including 7,455 homozygotes. There are 14,205 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 0.43 (7455 hom., 14205 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.25717311G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.429 AC: 47596 AN: 111040 Hom.: 7457 Cov.: 23 AF XY: 0.426 AC XY: 14180 AN XY: 33290

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.0917

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.429 AC: 47617 AN: 111093 Hom.: 7455 Cov.: 23 AF XY: 0.426 AC XY: 14205 AN XY: 33353

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.422

Alfa AF: 0.395 Hom.: 3106

Bravo AF: 0.444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.93
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4557887; hg19: chrX-25735428;