GeneBe

XR_945388.3:n.118+110489G>A

Variant names:

Variant summary

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

The XR_945388.3(LOC105370003):​n.118+110489G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,822 control chromosomes in the GnomAD database, including 8,250 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 0.32 ( 8250 hom., cov: 30)

Consequence

LOC105370003
XR_945388.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0110

Publications

3 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=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105370003XR_945388.3 linkn.118+110489G>A intron_variant Intron 1 of 3
LOC105370003XR_945389.3 linkn.118+110489G>A intron_variant Intron 1 of 3

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.321
AC:
48725
AN:
151704
Hom.:
8249
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.246
Gnomad AMI
AF:
0.252
Gnomad AMR
AF:
0.229
Gnomad ASJ
AF:
0.362
Gnomad EAS
AF:
0.272
Gnomad SAS
AF:
0.292
Gnomad FIN
AF:
0.461
Gnomad MID
AF:
0.285
Gnomad NFE
AF:
0.371
Gnomad OTH
AF:
0.320
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.321
AC:
48740
AN:
151822
Hom.:
8250
Cov.:
30
AF XY:
0.322
AC XY:
23852
AN XY:
74158
show subpopulations
African (AFR)
AF:
0.246
AC:
10172
AN:
41400
American (AMR)
AF:
0.229
AC:
3494
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
0.362
AC:
1255
AN:
3468
East Asian (EAS)
AF:
0.272
AC:
1398
AN:
5134
South Asian (SAS)
AF:
0.292
AC:
1399
AN:
4796
European-Finnish (FIN)
AF:
0.461
AC:
4857
AN:
10526
Middle Eastern (MID)
AF:
0.286
AC:
84
AN:
294
European-Non Finnish (NFE)
AF:
0.371
AC:
25169
AN:
67914
Other (OTH)
AF:
0.323
AC:
683
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1633
3266
4900
6533
8166
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
494
988
1482
1976
2470
<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:
0.324
Hom.:
5142
Bravo
AF:
0.301
Asia WGS
AF:
0.290
AC:
1010
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
2.7
DANN
Benign
0.79
PhyloP100
0.011

Splicing

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

Publications

Other links and lift over

dbSNP: rs7308283; hg19: chr12-116090264; API