XR_007086222.1:n.5765C>T

Variant summary

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

The XR_007086222.1(LOC124905974):​n.5765C>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 0.125 in 152,120 control chromosomes in the GnomAD database, including 1,431 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 0.13 ( 1431 hom., cov: 32)

Consequence

LOC124905974
XR_007086222.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0920

Publications

8 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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124905974XR_007086222.1 linkn.5765C>T non_coding_transcript_exon_variant Exon 1 of 2
LOC124905974XR_007086221.1 linkn.544+5221C>T intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000286427ENST00000657078.2 linkn.389+5370C>T intron_variant Intron 1 of 1
ENSG00000286427ENST00000840615.1 linkn.282+5370C>T intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.125
AC:
19006
AN:
152002
Hom.:
1433
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.204
Gnomad AMI
AF:
0.126
Gnomad AMR
AF:
0.0885
Gnomad ASJ
AF:
0.139
Gnomad EAS
AF:
0.000770
Gnomad SAS
AF:
0.127
Gnomad FIN
AF:
0.0375
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.108
Gnomad OTH
AF:
0.119
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.125
AC:
19015
AN:
152120
Hom.:
1431
Cov.:
32
AF XY:
0.120
AC XY:
8922
AN XY:
74372
show subpopulations
African (AFR)
AF:
0.204
AC:
8446
AN:
41454
American (AMR)
AF:
0.0884
AC:
1351
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.139
AC:
481
AN:
3470
East Asian (EAS)
AF:
0.000772
AC:
4
AN:
5180
South Asian (SAS)
AF:
0.127
AC:
608
AN:
4806
European-Finnish (FIN)
AF:
0.0375
AC:
398
AN:
10604
Middle Eastern (MID)
AF:
0.163
AC:
48
AN:
294
European-Non Finnish (NFE)
AF:
0.108
AC:
7314
AN:
67996
Other (OTH)
AF:
0.118
AC:
250
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
845
1689
2534
3378
4223
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
218
436
654
872
1090
<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:
0.109
Hom.:
704
Bravo
AF:
0.131
Asia WGS
AF:
0.0570
AC:
200
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.51
DANN
Benign
0.27
PhyloP100
-0.092

Splicing

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

Publications

Other links and lift over

dbSNP: rs7607490; hg19: chr2-12851120; API