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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902805	XM_047428004.1	c.52-1184A>G		intron_variant	Intron 1 of 3		XP_047283960.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;