rs4446880

Variant names:

• chrX-152531666-T-A
• rs4446880

Your query was ambiguous. Multiple possible variants found:

• chrX-152531666-T-A
• chrX-152531666-T-C

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 0.211 in 111,226 control chromosomes in the GnomAD database, including 1,840 homozygotes. There are 6,816 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 (1840 hom., 6816 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.211 AC: 23406 AN: 111170 Hom.: 1835 Cov.: 23

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0585

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.211 AC: 23424 AN: 111226 Hom.: 1840 Cov.: 23 AF XY: 0.204 AC XY: 6816 AN XY: 33456

African (AFR) AF: 0.213 AC: 6502 AN: 30591

American (AMR) AF: 0.309 AC: 3240 AN: 10488

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 764 AN: 2629

East Asian (EAS) AF: 0.252 AC: 880 AN: 3489

South Asian (SAS) AF: 0.219 AC: 575 AN: 2627

European-Finnish (FIN) AF: 0.131 AC: 789 AN: 6034

Middle Eastern (MID) AF: 0.205 AC: 44 AN: 215

European-Non Finnish (NFE) AF: 0.194 AC: 10259 AN: 52952

Other (OTH) AF: 0.218 AC: 331 AN: 1517

Alfa AF: 0.0449 Hom.: 183

Bravo AF: 0.227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.7
DANN	Benign	0.28
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4446880; hg19: chrX-151700138;