dbSNP rs7657356: UMLILO:n.160-10436C>T (chr4-73724067-C-T) – 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.160-10436C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0739 in 152,114 control chromosomes in the GnomAD database, including 666 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 0.074 ( 666 hom., cov: 32)

Consequence

UMLILO
ENST00000821867.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Publications

1 publications found

Variant links:

Genes affected

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

UMLILO links:

Genome browser will be placed here

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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 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.160-10436C>T		intron_variant	Intron 1 of 1
UMLILO	ENST00000821868.1 link	n.175+7366C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0739

AC:

11239

AN:

151996

Hom.:

667

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0722

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.0538

Gnomad ASJ

AF:

0.129

Gnomad EAS

AF:

0.308

Gnomad SAS

AF:

0.171

Gnomad FIN

AF:

0.0351

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.0576

Gnomad OTH

AF:

0.0863

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

GnomAD4 genome

AF:

0.0739

AC:

11236

AN:

152114

Hom.:

666

Cov.:

AF XY:

0.0759

AC XY:

5646

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.0721

AC:

2990

AN:

41494

American (AMR)

AF:

0.0539

AC:

823

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.129

AC:

447

AN:

3468

East Asian (EAS)

AF:

0.308

AC:

1591

AN:

5172

South Asian (SAS)

AF:

0.172

AC:

827

AN:

4816

European-Finnish (FIN)

AF:

0.0351

AC:

372

AN:

10592

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0575

AC:

3912

AN:

67984

Other (OTH)

AF:

0.0849

AC:

179

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

502

1004

1507

2009

2511

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

142

284

426

568

710

<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:

0.0638

Hom.:

470

Bravo

AF:

0.0759

Asia WGS

AF:

0.163

AC:

567

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

3.7

(source)

DANN

Benign

0.73

PhyloP100

-1.0

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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