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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.211 AC: 23406 AN: 111170 Hom.: 1835 Cov.: 23 AF XY: 0.204 AC XY: 6803 AN XY: 33390

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

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.218

Alfa AF: 0.0449 Hom.: 183

Bravo AF: 0.227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4446880; hg19: chrX-151700138;