X-139223625-A-G

Variant names:

• chrX-139223625-A-G
• rs12556103

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;