rs4446880

chrX-152531666-T-AchrX-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;