XR_926680.3:n.2192T>C

Variant summary

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

The XR_926680.3(LOC105375010):​n.2192T>C 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 0.161 in 152,210 control chromosomes in the GnomAD database, including 2,007 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 0.16 ( 2007 hom., cov: 33)

Consequence

LOC105375010
XR_926680.3 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.91

Publications

22 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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105375010XR_926680.3 linkn.2192T>C non_coding_transcript_exon_variant Exon 3 of 3
LOC105375010XR_926682.3 linkn.711T>C non_coding_transcript_exon_variant Exon 3 of 3
LOC105375010XR_926681.2 linkn.1781-241T>C intron_variant Intron 3 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.161
AC:
24545
AN:
152092
Hom.:
2002
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.145
Gnomad AMI
AF:
0.183
Gnomad AMR
AF:
0.185
Gnomad ASJ
AF:
0.173
Gnomad EAS
AF:
0.213
Gnomad SAS
AF:
0.158
Gnomad FIN
AF:
0.135
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.166
Gnomad OTH
AF:
0.153
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.161
AC:
24554
AN:
152210
Hom.:
2007
Cov.:
33
AF XY:
0.160
AC XY:
11913
AN XY:
74410
show subpopulations
African (AFR)
AF:
0.145
AC:
6029
AN:
41536
American (AMR)
AF:
0.185
AC:
2829
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.173
AC:
599
AN:
3466
East Asian (EAS)
AF:
0.212
AC:
1100
AN:
5180
South Asian (SAS)
AF:
0.156
AC:
753
AN:
4820
European-Finnish (FIN)
AF:
0.135
AC:
1434
AN:
10594
Middle Eastern (MID)
AF:
0.139
AC:
41
AN:
294
European-Non Finnish (NFE)
AF:
0.166
AC:
11266
AN:
68018
Other (OTH)
AF:
0.159
AC:
336
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1086
2172
3257
4343
5429
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
260
520
780
1040
1300
<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:
0.166
Hom.:
8748
Bravo
AF:
0.164
Asia WGS
AF:
0.261
AC:
905
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.1
DANN
Benign
0.45
PhyloP100
-1.9

Splicing

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

Publications

Other links and lift over

dbSNP: rs2394186; hg19: chr6-29816421; API