rs12506479

Variant names:

• chr4-73726444-T-C
• rs12506479
• ENST00000821867.1:n.160-8059T>C

Variant summary

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

The ENST00000821867.1(UMLILO):​n.160-8059T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,164 control chromosomes in the GnomAD database, including 5,949 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 0.27 (5949 hom., cov: 32)
• Consequence: UMLILO ENST00000821867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 14 publications found

Genes affected

UMLILO (HGNC:51824): (upstream master lncRNA of the inflammatory chemokine locus)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821867.1. You can select a different transcript below to see updated ACMG assignments.

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
	UMLILO	ENST00000821867.1		n.160-8059T>C		intron	N/A
	UMLILO	ENST00000821868.1		n.176-8059T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41480 AN: 152046 Hom.: 5937 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.273 AC: 41523 AN: 152164 Hom.: 5949 Cov.: 32 AF XY: 0.279 AC XY: 20734 AN XY: 74402

African (AFR) AF: 0.215 AC: 8926 AN: 41524

American (AMR) AF: 0.383 AC: 5848 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3470

East Asian (EAS) AF: 0.432 AC: 2239 AN: 5178

South Asian (SAS) AF: 0.322 AC: 1554 AN: 4824

European-Finnish (FIN) AF: 0.286 AC: 3026 AN: 10584

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17933 AN: 67980

Other (OTH) AF: 0.265 AC: 559 AN: 2110

Alfa AF: 0.272 Hom.: 11328

Bravo AF: 0.279

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.040
DANN	Benign	0.37
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12506479; hg19: chr4-74592161;