rs11796704

Variant names:

• chrX-52148331-G-A
• rs11796704

Your query was ambiguous. Multiple possible variants found:

• chrX-52148331-G-A
• chrX-52148331-G-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 0.156 in 110,432 control chromosomes in the GnomAD database, including 1,006 homozygotes. There are 4,882 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 0.16 (1006 hom., 4882 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 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: 0.156 AC: 17240 AN: 110385 Hom.: 1005 Cov.: 22 AF XY: 0.149 AC XY: 4870 AN XY: 32775

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0190

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.156 AC: 17251 AN: 110432 Hom.: 1006 Cov.: 22 AF XY: 0.149 AC XY: 4882 AN XY: 32832

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0190

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.147

Alfa AF: 0.0844 Hom.: 426

Bravo AF: 0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.33
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11796704; hg19: chrX-51891427;