dbSNP rs1881457: TH2LCRR:n.119T>G (chr5-132656717-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000814671.1(TH2LCRR):n.119T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,468 control chromosomes in the GnomAD database, including 3,331 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 0.21 ( 3318 hom., cov: 32)

Exomes 𝑓: 0.21 ( 13 hom. )

Consequence

TH2LCRR
ENST00000814671.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.320

Publications

98 publications found

Variant links:

Genes affected

TH2LCRR (HGNC:40495): (T helper type 2 locus control region associated RNA)

TH2LCRR links:

IL13 (HGNC:5973): (interleukin 13) This gene encodes an immunoregulatory cytokine produced primarily by activated Th2 cells. This cytokine is involved in several stages of B-cell maturation and differentiation. It up-regulates CD23 and MHC class II expression, and promotes IgE isotype switching of B cells. This cytokine down-regulates macrophage activity, thereby inhibits the production of pro-inflammatory cytokines and chemokines. This cytokine is found to be critical to the pathogenesis of allergen-induced asthma but operates through mechanisms independent of IgE and eosinophils. This gene, IL3, IL5, IL4, and CSF2 form a cytokine gene cluster on chromosome 5q, with this gene particularly close to IL4. [provided by RefSeq, Jul 2008]

IL13 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
IL13	NM_001354991.2 link	c.-93+87A>C	intron_variant	Intron 1 of 4	NP_001341920.1
IL13	NM_001354992.2 link	c.-272+87A>C	intron_variant	Intron 1 of 5	NP_001341921.1
IL13	NM_001354993.2 link	c.-201+87A>C	intron_variant	Intron 1 of 4	NP_001341922.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TH2LCRR	ENST00000814671.1 link	n.119T>G	non_coding_transcript_exon_variant	Exon 1 of 3
TH2LCRR	ENST00000814681.1 link	n.107T>G	non_coding_transcript_exon_variant	Exon 1 of 2
TH2LCRR	ENST00000435042.1 link	n.94+7462T>G	intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31368

AN:

150856

Hom.:

3310

Cov.:

show subpopulations

Gnomad AFR

AF:

0.199

Gnomad AMI

AF:

0.122

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.244

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.264

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.204

GnomAD4 exome

AF:

0.209

AC:

103

AN:

494

Hom.:

AF XY:

0.209

AC XY:

AN XY:

358

show subpopulations

African (AFR)

AF:

0.0833

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.188

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.200

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.207

AC:

AN:

400

Other (OTH)

AF:

0.278

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.539

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.208

AC:

31413

AN:

150974

Hom.:

3318

Cov.:

AF XY:

0.209

AC XY:

15450

AN XY:

73836

show subpopulations

African (AFR)

AF:

0.199

AC:

8055

AN:

40378

American (AMR)

AF:

0.195

AC:

2980

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

887

AN:

3470

East Asian (EAS)

AF:

0.245

AC:

1254

AN:

5128

South Asian (SAS)

AF:

0.220

AC:

1061

AN:

4826

European-Finnish (FIN)

AF:

0.236

AC:

2504

AN:

10602

Middle Eastern (MID)

AF:

0.264

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.207

AC:

14059

AN:

67972

Other (OTH)

AF:

0.202

AC:

425

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1289

2577

3866

5154

6443

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.205

Hom.:

3107

Bravo

AF:

0.202

Asia WGS

AF:

0.222

AC:

774

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.9

(source)

DANN

Benign

0.84

PhyloP100

-0.32

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over