X-100527829-T-G

Variant names:

• chrX-100527829-T-G
• rs5921594

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 0.444 in 109,347 control chromosomes in the GnomAD database, including 8,378 homozygotes. There are 13,659 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 0.44 (8378 hom., 13659 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 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: 0.443 AC: 48468 AN: 109292 Hom.: 8373 Cov.: 22

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.444 AC: 48524 AN: 109347 Hom.: 8378 Cov.: 22 AF XY: 0.431 AC XY: 13659 AN XY: 31685

African (AFR) AF: 0.606 AC: 18137 AN: 29912

American (AMR) AF: 0.402 AC: 4115 AN: 10225

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1071 AN: 2628

East Asian (EAS) AF: 0.152 AC: 526 AN: 3468

South Asian (SAS) AF: 0.547 AC: 1362 AN: 2489

European-Finnish (FIN) AF: 0.388 AC: 2224 AN: 5729

Middle Eastern (MID) AF: 0.321 AC: 68 AN: 212

European-Non Finnish (NFE) AF: 0.384 AC: 20151 AN: 52520

Other (OTH) AF: 0.397 AC: 592 AN: 1490

Alfa AF: 0.411 Hom.: 51798

Bravo AF: 0.451

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.34
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs5921594; hg19: chrX-99782826;