X-139223625-A-G

Position:

• chrX-139223625-A-G

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 0.33 in 110,274 control chromosomes in the GnomAD database, including 4,919 homozygotes. There are 10,556 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 0.33 (4919 hom., 10556 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.436 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: 0.330 AC: 36428 AN: 110224 Hom.: 4927 Cov.: 22 AF XY: 0.325 AC XY: 10545 AN XY: 32490

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.330 AC: 36418 AN: 110274 Hom.: 4919 Cov.: 22 AF XY: 0.324 AC XY: 10556 AN XY: 32550

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.358

Alfa AF: 0.391 Hom.: 17512

Bravo AF: 0.338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12556103; hg19: chrX-138305787;