rs1883921

Variant names:

• chrX-115471502-C-G
• rs1883921

Your query was ambiguous. Multiple possible variants found:

• chrX-115471502-C-G
• chrX-115471502-C-T

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 0.498 in 110,590 control chromosomes in the GnomAD database, including 11,061 homozygotes. There are 16,660 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 0.50 (11061 hom., 16660 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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: 0.498 AC: 55048 AN: 110534 Hom.: 11068 Cov.: 23

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.511

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.498 AC: 55058 AN: 110590 Hom.: 11061 Cov.: 23 AF XY: 0.507 AC XY: 16660 AN XY: 32860

African (AFR) AF: 0.193 AC: 5889 AN: 30490

American (AMR) AF: 0.549 AC: 5709 AN: 10402

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1139 AN: 2629

East Asian (EAS) AF: 0.942 AC: 3255 AN: 3456

South Asian (SAS) AF: 0.776 AC: 1995 AN: 2572

European-Finnish (FIN) AF: 0.619 AC: 3600 AN: 5818

Middle Eastern (MID) AF: 0.502 AC: 106 AN: 211

European-Non Finnish (NFE) AF: 0.608 AC: 32099 AN: 52820

Other (OTH) AF: 0.538 AC: 814 AN: 1513

Alfa AF: 0.531 Hom.: 3871

Bravo AF: 0.479

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1883921; hg19: chrX-114706218;