XR_007063492.1:n.5382C>T

Variant summary

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

The XR_007063492.1(LOC105378258):​n.5382C>T 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 0.0529 in 152,302 control chromosomes in the GnomAD database, including 268 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 0.053 ( 268 hom., cov: 32)

Consequence

LOC105378258
XR_007063492.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.791

Publications

4 publications found
Variant links:
Genes affected

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=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0881 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105378258XR_007063492.1 linkn.5382C>T non_coding_transcript_exon_variant Exon 1 of 4
LOC105378258XR_945451.4 linkn.5382C>T non_coding_transcript_exon_variant Exon 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000308947ENST00000837477.1 linkn.540+199G>A intron_variant Intron 2 of 2
ENSG00000308932ENST00000837362.1 linkn.*243C>T downstream_gene_variant
ENSG00000308932ENST00000837363.1 linkn.*243C>T downstream_gene_variant
ENSG00000308932ENST00000837364.1 linkn.*243C>T downstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.0529
AC:
8052
AN:
152184
Hom.:
268
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0241
Gnomad AMI
AF:
0.0956
Gnomad AMR
AF:
0.0678
Gnomad ASJ
AF:
0.0400
Gnomad EAS
AF:
0.0540
Gnomad SAS
AF:
0.0945
Gnomad FIN
AF:
0.0538
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0638
Gnomad OTH
AF:
0.0606
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0529
AC:
8063
AN:
152302
Hom.:
268
Cov.:
32
AF XY:
0.0534
AC XY:
3973
AN XY:
74470
show subpopulations
African (AFR)
AF:
0.0242
AC:
1007
AN:
41570
American (AMR)
AF:
0.0677
AC:
1035
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
0.0400
AC:
139
AN:
3472
East Asian (EAS)
AF:
0.0545
AC:
282
AN:
5176
South Asian (SAS)
AF:
0.0952
AC:
460
AN:
4830
European-Finnish (FIN)
AF:
0.0538
AC:
571
AN:
10610
Middle Eastern (MID)
AF:
0.0476
AC:
14
AN:
294
European-Non Finnish (NFE)
AF:
0.0638
AC:
4342
AN:
68026
Other (OTH)
AF:
0.0595
AC:
126
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
399
798
1196
1595
1994
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
98
196
294
392
490
<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:
0.0515
Hom.:
33
Bravo
AF:
0.0514
Asia WGS
AF:
0.0790
AC:
275
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.15
DANN
Benign
0.54
PhyloP100
-0.79

Splicing

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

Publications

Other links and lift over

dbSNP: rs12819523; hg19: chr12-121525417; API