rs11094388

Variant names:

• chrX-146958495-A-G
• rs11094388
• ENST00000790926.1:n.1061+3320A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000790926.1(ENSG00000289591):​n.1061+3320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000289591 ENST00000790926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 1 publications found

Genes affected

ENSG00000289591 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790926.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000289591	ENST00000790926.1		n.1061+3320A>G		intron	N/A
	ENSG00000289591	ENST00000790927.1		n.1039+3320A>G		intron	N/A
	ENSG00000289591	ENST00000790928.1		n.754+3320A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 35423 AN: 108119 Hom.: 5021 Cov.: 21

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

African (AFR) AF: 0.179 AC: 4996 AN: 27970

American (AMR) AF: 0.287 AC: 2969 AN: 10337

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1076 AN: 2637

East Asian (EAS) AF: 0.177 AC: 623 AN: 3511

South Asian (SAS) AF: 0.194 AC: 525 AN: 2702

European-Finnish (FIN) AF: 0.478 AC: 2776 AN: 5809

Middle Eastern (MID) AF: 0.371 AC: 78 AN: 210

European-Non Finnish (NFE) AF: 0.408 AC: 21537 AN: 52809

Other (OTH) AF: 0.313 AC: 463 AN: 1480

Alfa AF: 0.373 Hom.: 8676

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.24
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs11094388; hg19: chrX-146040013;