rs12286521

Variant names:

• chr11-573554-A-G
• rs12286521
• XM_047428004.1:c.52-1184A>G

Variant summary

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

The XM_047428004.1(LOC124902805):​c.52-1184A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,450 control chromosomes in the GnomAD database, including 12,209 homozygotes. 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 0.39 (12209 hom., cov: 29)
• Consequence: LOC124902805 XM_047428004.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 18 publications found

Genes affected

LOC124902805 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 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: 0.391 AC: 59128 AN: 151332 Hom.: 12172 Cov.: 29

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.391 AC: 59228 AN: 151450 Hom.: 12209 Cov.: 29 AF XY: 0.384 AC XY: 28435 AN XY: 74024

African (AFR) AF: 0.512 AC: 21075 AN: 41150

American (AMR) AF: 0.484 AC: 7365 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3468

East Asian (EAS) AF: 0.228 AC: 1173 AN: 5136

South Asian (SAS) AF: 0.279 AC: 1332 AN: 4782

European-Finnish (FIN) AF: 0.232 AC: 2453 AN: 10568

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.348 AC: 23584 AN: 67812

Other (OTH) AF: 0.391 AC: 820 AN: 2098

Alfa AF: 0.366 Hom.: 36882

Bravo AF: 0.415

Asia WGS AF: 0.332 AC: 1152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.38
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12286521; hg19: chr11-573554;