GeneBe

XR_935583.2:n.117+3106C>A

Variant names:

Variant summary

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

The XR_935583.2(LOC105372169):​n.117+3106C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 150,972 control chromosomes in the GnomAD database, including 16,459 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 0.46 ( 16459 hom., cov: 32)

Consequence

LOC105372169
XR_935583.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.358

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=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105372169XR_935583.2 linkn.117+3106C>A intron_variant Intron 1 of 4

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.464
AC:
70063
AN:
150854
Hom.:
16443
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.511
Gnomad AMI
AF:
0.582
Gnomad AMR
AF:
0.406
Gnomad ASJ
AF:
0.564
Gnomad EAS
AF:
0.593
Gnomad SAS
AF:
0.466
Gnomad FIN
AF:
0.403
Gnomad MID
AF:
0.478
Gnomad NFE
AF:
0.442
Gnomad OTH
AF:
0.457
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.464
AC:
70121
AN:
150972
Hom.:
16459
Cov.:
32
AF XY:
0.463
AC XY:
34197
AN XY:
73786
show subpopulations
African (AFR)
AF:
0.511
AC:
21146
AN:
41360
American (AMR)
AF:
0.405
AC:
6124
AN:
15104
Ashkenazi Jewish (ASJ)
AF:
0.564
AC:
1943
AN:
3444
East Asian (EAS)
AF:
0.594
AC:
3057
AN:
5144
South Asian (SAS)
AF:
0.465
AC:
2239
AN:
4818
European-Finnish (FIN)
AF:
0.403
AC:
4253
AN:
10546
Middle Eastern (MID)
AF:
0.473
AC:
139
AN:
294
European-Non Finnish (NFE)
AF:
0.442
AC:
29732
AN:
67250
Other (OTH)
AF:
0.456
AC:
957
AN:
2100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1922
3844
5766
7688
9610
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
662
1324
1986
2648
3310
<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:
0.447
Hom.:
2607
Bravo
AF:
0.472
Asia WGS
AF:
0.461
AC:
1597
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.40
DANN
Benign
0.63
PhyloP100
-0.36

Splicing

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

Publications

Other links and lift over

dbSNP: rs1444067; hg19: chr18-63170686; API