rs12555969

Variant names:

• chrX-146302374-C-T
• rs12555969

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 0.36 in 110,039 control chromosomes in the GnomAD database, including 5,805 homozygotes. There are 11,849 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 0.36 (5805 hom., 11849 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.27
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.505 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: 0.360 AC: 39621 AN: 109987 Hom.: 5799 Cov.: 22

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.360 AC: 39640 AN: 110039 Hom.: 5805 Cov.: 22 AF XY: 0.367 AC XY: 11849 AN XY: 32299

African (AFR) AF: 0.152 AC: 4621 AN: 30481

American (AMR) AF: 0.517 AC: 5274 AN: 10200

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1118 AN: 2633

East Asian (EAS) AF: 0.462 AC: 1573 AN: 3402

South Asian (SAS) AF: 0.359 AC: 929 AN: 2588

European-Finnish (FIN) AF: 0.549 AC: 3104 AN: 5651

Middle Eastern (MID) AF: 0.330 AC: 70 AN: 212

European-Non Finnish (NFE) AF: 0.421 AC: 22197 AN: 52695

Other (OTH) AF: 0.391 AC: 588 AN: 1502

Alfa AF: 0.405 Hom.: 30728

Bravo AF: 0.358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.051
DANN	Benign	0.40
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs12555969; hg19: chrX-145383892;