GeneBe

2-112906296-A-G

Variant names:

Variant summary

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

The XR_007087196.1(LOC124906068):​n.91-272T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.964 in 152,280 control chromosomes in the GnomAD database, including 70,965 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 0.96 ( 70965 hom., cov: 32)

Consequence

LOC124906068
XR_007087196.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.546

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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124906068XR_007087196.1 linkn.91-272T>C intron_variant Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.964
AC:
146692
AN:
152162
Hom.:
70913
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.877
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.985
Gnomad ASJ
AF:
0.984
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
0.999
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
0.984
Gnomad NFE
AF:
0.999
Gnomad OTH
AF:
0.979
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.964
AC:
146801
AN:
152280
Hom.:
70965
Cov.:
32
AF XY:
0.966
AC XY:
71904
AN XY:
74460
show subpopulations
African (AFR)
AF:
0.878
AC:
36454
AN:
41538
American (AMR)
AF:
0.985
AC:
15066
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.984
AC:
3415
AN:
3470
East Asian (EAS)
AF:
1.00
AC:
5194
AN:
5194
South Asian (SAS)
AF:
0.999
AC:
4822
AN:
4826
European-Finnish (FIN)
AF:
1.00
AC:
10612
AN:
10612
Middle Eastern (MID)
AF:
0.986
AC:
290
AN:
294
European-Non Finnish (NFE)
AF:
0.999
AC:
67965
AN:
68030
Other (OTH)
AF:
0.979
AC:
2071
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
252
504
755
1007
1259
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
912
1824
2736
3648
4560
<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:
0.975
Hom.:
24883
Bravo
AF:
0.959
Asia WGS
AF:
0.992
AC:
3451
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.8
DANN
Benign
0.81
PhyloP100
-0.55

Splicing

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

Publications

Other links and lift over

dbSNP: rs2708973; hg19: chr2-113663873; API