rs1886827

Variant names:

• chrX-98410973-T-A
• rs1886827

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 0.31 in 110,889 control chromosomes in the GnomAD database, including 4,200 homozygotes. There are 10,340 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 0.31 (4200 hom., 10340 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.310 AC: 34325 AN: 110839 Hom.: 4210 Cov.: 23

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.310 AC: 34325 AN: 110889 Hom.: 4200 Cov.: 23 AF XY: 0.311 AC XY: 10340 AN XY: 33199

African (AFR) AF: 0.218 AC: 6686 AN: 30649

American (AMR) AF: 0.476 AC: 4924 AN: 10354

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 942 AN: 2634

East Asian (EAS) AF: 0.757 AC: 2629 AN: 3471

South Asian (SAS) AF: 0.529 AC: 1390 AN: 2630

European-Finnish (FIN) AF: 0.216 AC: 1294 AN: 5980

Middle Eastern (MID) AF: 0.295 AC: 64 AN: 217

European-Non Finnish (NFE) AF: 0.298 AC: 15749 AN: 52784

Other (OTH) AF: 0.352 AC: 526 AN: 1494

Alfa AF: 0.301 Hom.: 1902

Bravo AF: 0.330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.31
DANN	Benign	0.58
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1886827; hg19: chrX-97665971;