Genetic Variant UMLILO:n.160-8059T>C (chr4-73726444-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14

Publications

14 publications found

Variant links:

Genes affected

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

UMLILO links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UMLILO	ENST00000821867.1 link	n.160-8059T>C		intron_variant	Intron 1 of 1
UMLILO	ENST00000821868.1 link	n.176-8059T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.273

AC:

41480

AN:

152046

Hom.:

5937

Cov.:

show subpopulations

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.:

AF XY:

0.279

AC XY:

20734

AN XY:

74402

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.264

AC:

17933

AN:

67980

Other (OTH)

AF:

0.265

AC:

559

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1543

3086

4628

6171

7714

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

432

864

1296

1728

2160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.040

(source)

DANN

Benign

0.37

PhyloP100

-1.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over