rs12387240

Variant names:

• chrX-144413775-C-A
• rs12387240

Your query was ambiguous. Multiple possible variants found:

• chrX-144413775-C-A
• chrX-144413775-C-G

Variant summary

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

The variant allele was found at a frequency of 0.163 in 111,544 control chromosomes in the GnomAD database, including 1,142 homozygotes. There are 5,341 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 (1142 hom., 5341 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.163 AC: 18202 AN: 111488 Hom.: 1140 Cov.: 23

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0844

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.128

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.163 AC: 18203 AN: 111544 Hom.: 1142 Cov.: 23 AF XY: 0.158 AC XY: 5341 AN XY: 33800

African (AFR) AF: 0.143 AC: 4391 AN: 30738

American (AMR) AF: 0.237 AC: 2497 AN: 10551

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 404 AN: 2644

East Asian (EAS) AF: 0.0841 AC: 294 AN: 3496

South Asian (SAS) AF: 0.212 AC: 567 AN: 2676

European-Finnish (FIN) AF: 0.117 AC: 703 AN: 6009

Middle Eastern (MID) AF: 0.121 AC: 26 AN: 214

European-Non Finnish (NFE) AF: 0.167 AC: 8867 AN: 53019

Other (OTH) AF: 0.178 AC: 272 AN: 1525

Alfa AF: 0.173 Hom.: 15597

Bravo AF: 0.174

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.25
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs12387240; hg19: chrX-143496870;