X-139223625-A-G

Variant names:

• chrX-139223625-A-G
• rs12556103

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.330 AC: 36428 AN: 110224 Hom.: 4927 Cov.: 22

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

African (AFR) AF: 0.137 AC: 4182 AN: 30490

American (AMR) AF: 0.447 AC: 4602 AN: 10301

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1076 AN: 2628

East Asian (EAS) AF: 0.388 AC: 1335 AN: 3444

South Asian (SAS) AF: 0.429 AC: 1088 AN: 2536

European-Finnish (FIN) AF: 0.358 AC: 2080 AN: 5803

Middle Eastern (MID) AF: 0.514 AC: 108 AN: 210

European-Non Finnish (NFE) AF: 0.400 AC: 21061 AN: 52694

Other (OTH) AF: 0.358 AC: 537 AN: 1500

Alfa AF: 0.379 Hom.: 25272

Bravo AF: 0.338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.76
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs12556103; hg19: chrX-138305787;