rs11094388

Variant names:

• chrX-146958495-A-G
• rs11094388

Your query was ambiguous. Multiple possible variants found:

• chrX-146958495-A-G
• chrX-146958495-A-T

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 0.327 in 108,142 control chromosomes in the GnomAD database, including 5,021 homozygotes. There are 10,297 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 0.33 (5021 hom., 10297 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.403 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: 0.328 AC: 35423 AN: 108119 Hom.: 5021 Cov.: 21 AF XY: 0.324 AC XY: 10292 AN XY: 31745

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.327 AC: 35416 AN: 108142 Hom.: 5021 Cov.: 21 AF XY: 0.324 AC XY: 10297 AN XY: 31778

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.313

Alfa AF: 0.371 Hom.: 7685

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11094388; hg19: chrX-146040013;