rs4827881

Variant names:

• chrX-100874684-C-A
• rs4827881

Your query was ambiguous. Multiple possible variants found:

• chrX-100874684-C-A
• chrX-100874684-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 0.21 in 111,025 control chromosomes in the GnomAD database, including 1,890 homozygotes. There are 7,013 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 0.21 (1890 hom., 7013 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 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: 0.210 AC: 23262 AN: 110970 Hom.: 1889 Cov.: 23

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0914

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.219

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.210 AC: 23283 AN: 111025 Hom.: 1890 Cov.: 23 AF XY: 0.211 AC XY: 7013 AN XY: 33269

African (AFR) AF: 0.129 AC: 3965 AN: 30624

American (AMR) AF: 0.231 AC: 2397 AN: 10394

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 632 AN: 2625

East Asian (EAS) AF: 0.0911 AC: 320 AN: 3511

South Asian (SAS) AF: 0.145 AC: 382 AN: 2636

European-Finnish (FIN) AF: 0.337 AC: 1974 AN: 5865

Middle Eastern (MID) AF: 0.208 AC: 44 AN: 212

European-Non Finnish (NFE) AF: 0.248 AC: 13129 AN: 52963

Other (OTH) AF: 0.215 AC: 326 AN: 1519

Alfa AF: 0.222 Hom.: 19671

Bravo AF: 0.201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.70
PhyloP100		-0.16
PromoterAI		0.045	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4827881; hg19: chrX-100129673;