XR_001754065.2:n.11495C>T

Variant summary

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

The XR_001754065.2(LOC105372310):​n.11495C>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 0.304 in 151,776 control chromosomes in the GnomAD database, including 8,541 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 0.30 ( 8541 hom., cov: 31)

Consequence

LOC105372310
XR_001754065.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

9 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=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105372310XR_001754065.2 linkn.11495C>T non_coding_transcript_exon_variant Exon 5 of 6
LOC105372310XR_007067164.1 linkn.11495C>T non_coding_transcript_exon_variant Exon 5 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000267383ENST00000585498.2 linkn.173+19986C>T intron_variant Intron 1 of 3 2
ENSG00000267383ENST00000586657.2 linkn.207+19986C>T intron_variant Intron 1 of 2 4
ENSG00000267383ENST00000592022.1 linkn.98-986C>T intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
AF:
0.304
AC:
46083
AN:
151660
Hom.:
8511
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.499
Gnomad AMI
AF:
0.121
Gnomad AMR
AF:
0.314
Gnomad ASJ
AF:
0.198
Gnomad EAS
AF:
0.477
Gnomad SAS
AF:
0.296
Gnomad FIN
AF:
0.239
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.189
Gnomad OTH
AF:
0.281
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.304
AC:
46158
AN:
151776
Hom.:
8541
Cov.:
31
AF XY:
0.307
AC XY:
22772
AN XY:
74158
show subpopulations
African (AFR)
AF:
0.500
AC:
20664
AN:
41366
American (AMR)
AF:
0.314
AC:
4785
AN:
15240
Ashkenazi Jewish (ASJ)
AF:
0.198
AC:
685
AN:
3468
East Asian (EAS)
AF:
0.478
AC:
2459
AN:
5146
South Asian (SAS)
AF:
0.296
AC:
1427
AN:
4820
European-Finnish (FIN)
AF:
0.239
AC:
2506
AN:
10496
Middle Eastern (MID)
AF:
0.265
AC:
78
AN:
294
European-Non Finnish (NFE)
AF:
0.189
AC:
12854
AN:
67924
Other (OTH)
AF:
0.279
AC:
590
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1481
2962
4443
5924
7405
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
448
896
1344
1792
2240
<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:
0.227
Hom.:
17326
Bravo
AF:
0.320
Asia WGS
AF:
0.413
AC:
1435
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
0.59
DANN
Benign
0.53
PhyloP100
-1.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs1654260; hg19: chr19-20329111; API