GeneBe

5-132648366-A-G

Variant names:

Variant summary

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

The ENST00000458509.1(TH2LCRR):​n.105-6084T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,202 control chromosomes in the GnomAD database, including 2,539 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 0.18 ( 2539 hom., cov: 32)

Consequence

TH2LCRR
ENST00000458509.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.461

Publications

28 publications found
Variant links:
Genes affected
TH2LCRR (HGNC:40495): (T helper type 2 locus control region associated RNA)

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=-0.74).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TH2LCRRNR_132125.1 linkn.105-6084T>C intron_variant Intron 1 of 2
TH2LCRRNR_132126.1 linkn.174+7353T>C intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TH2LCRRENST00000458509.1 linkn.105-6084T>C intron_variant Intron 1 of 2 1
TH2LCRRENST00000417516.2 linkn.474+7353T>C intron_variant Intron 1 of 1 2
TH2LCRRENST00000435042.1 linkn.95-6084T>C intron_variant Intron 1 of 3 5

Frequencies

GnomAD3 genomes
AF:
0.177
AC:
26960
AN:
152084
Hom.:
2536
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.124
Gnomad AMI
AF:
0.122
Gnomad AMR
AF:
0.139
Gnomad ASJ
AF:
0.220
Gnomad EAS
AF:
0.176
Gnomad SAS
AF:
0.214
Gnomad FIN
AF:
0.233
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.205
Gnomad OTH
AF:
0.185
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.177
AC:
26977
AN:
152202
Hom.:
2539
Cov.:
32
AF XY:
0.179
AC XY:
13304
AN XY:
74400
show subpopulations
African (AFR)
AF:
0.124
AC:
5143
AN:
41542
American (AMR)
AF:
0.139
AC:
2123
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.220
AC:
762
AN:
3470
East Asian (EAS)
AF:
0.177
AC:
916
AN:
5184
South Asian (SAS)
AF:
0.214
AC:
1034
AN:
4826
European-Finnish (FIN)
AF:
0.233
AC:
2466
AN:
10578
Middle Eastern (MID)
AF:
0.241
AC:
71
AN:
294
European-Non Finnish (NFE)
AF:
0.205
AC:
13965
AN:
67992
Other (OTH)
AF:
0.183
AC:
386
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1142
2284
3426
4568
5710
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
306
612
918
1224
1530
<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:
0.190
Hom.:
531
Bravo
AF:
0.165
Asia WGS
AF:
0.186
AC:
649
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
3.0
DANN
Benign
0.76
PhyloP100
0.46
Mutation Taster
=100/0
polymorphism

Splicing

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

Publications

Other links and lift over

dbSNP: rs2158177; hg19: chr5-131984058; API