GeneBe

7-156017909-C-G

Variant names:

Variant summary

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

The XR_928242.3(LOC105375597):​n.191+1457C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,236 control chromosomes in the GnomAD database, including 16,130 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 0.45 ( 16130 hom., cov: 35)

Consequence

LOC105375597
XR_928242.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.533

Publications

2 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=-1.01).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105375597XR_928242.3 linkn.191+1457C>G intron_variant Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.455
AC:
69148
AN:
152118
Hom.:
16108
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.377
Gnomad AMI
AF:
0.650
Gnomad AMR
AF:
0.381
Gnomad ASJ
AF:
0.504
Gnomad EAS
AF:
0.448
Gnomad SAS
AF:
0.439
Gnomad FIN
AF:
0.516
Gnomad MID
AF:
0.506
Gnomad NFE
AF:
0.505
Gnomad OTH
AF:
0.455
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.455
AC:
69212
AN:
152236
Hom.:
16130
Cov.:
35
AF XY:
0.454
AC XY:
33825
AN XY:
74428
show subpopulations
African (AFR)
AF:
0.377
AC:
15660
AN:
41534
American (AMR)
AF:
0.380
AC:
5819
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
0.504
AC:
1751
AN:
3472
East Asian (EAS)
AF:
0.449
AC:
2323
AN:
5178
South Asian (SAS)
AF:
0.438
AC:
2117
AN:
4830
European-Finnish (FIN)
AF:
0.516
AC:
5463
AN:
10596
Middle Eastern (MID)
AF:
0.517
AC:
152
AN:
294
European-Non Finnish (NFE)
AF:
0.505
AC:
34361
AN:
68006
Other (OTH)
AF:
0.460
AC:
973
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
2013
4025
6038
8050
10063
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
638
1276
1914
2552
3190
<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:
0.362
Hom.:
1060
Bravo
AF:
0.437
Asia WGS
AF:
0.467
AC:
1623
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
0.077
DANN
Benign
0.35
PhyloP100
-0.53

Splicing

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

Publications

Other links and lift over

dbSNP: rs7784332; hg19: chr7-155810603; API