chrX-84528171-A-G

Variant names:

• chrX-84528171-A-G
• rs10521369

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 0.507 in 109,268 control chromosomes in the GnomAD database, including 11,091 homozygotes. There are 16,070 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 0.51 (11091 hom., 16070 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.609 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: 0.507 AC: 55361 AN: 109217 Hom.: 11092 Cov.: 22

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.626

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.507 AC: 55380 AN: 109268 Hom.: 11091 Cov.: 22 AF XY: 0.505 AC XY: 16070 AN XY: 31830

African (AFR) AF: 0.251 AC: 7615 AN: 30342

American (AMR) AF: 0.617 AC: 6272 AN: 10164

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 1809 AN: 2617

East Asian (EAS) AF: 0.439 AC: 1511 AN: 3440

South Asian (SAS) AF: 0.626 AC: 1606 AN: 2566

European-Finnish (FIN) AF: 0.561 AC: 3202 AN: 5703

Middle Eastern (MID) AF: 0.621 AC: 133 AN: 214

European-Non Finnish (NFE) AF: 0.614 AC: 31985 AN: 52059

Other (OTH) AF: 0.540 AC: 805 AN: 1492

Alfa AF: 0.548 Hom.: 4113

Bravo AF: 0.502

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.58
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs10521369; hg19: chrX-83783179;