GeneBe

XR_007058226.1:n.165-37T>G

Variant names:

Variant summary

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

The XR_007058226.1(LOC124900757):​n.165-37T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,042 control chromosomes in the GnomAD database, including 28,938 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 0.61 ( 28938 hom., cov: 31)

Consequence

LOC124900757
XR_007058226.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.581

Publications

11 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=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124900757XR_007058226.1 linkn.165-37T>G intron_variant Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.608
AC:
92326
AN:
151924
Hom.:
28937
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.459
Gnomad AMI
AF:
0.549
Gnomad AMR
AF:
0.554
Gnomad ASJ
AF:
0.641
Gnomad EAS
AF:
0.582
Gnomad SAS
AF:
0.621
Gnomad FIN
AF:
0.658
Gnomad MID
AF:
0.554
Gnomad NFE
AF:
0.703
Gnomad OTH
AF:
0.609
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.607
AC:
92365
AN:
152042
Hom.:
28938
Cov.:
31
AF XY:
0.605
AC XY:
44999
AN XY:
74326
show subpopulations
African (AFR)
AF:
0.458
AC:
19001
AN:
41442
American (AMR)
AF:
0.554
AC:
8453
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
0.641
AC:
2227
AN:
3472
East Asian (EAS)
AF:
0.581
AC:
3012
AN:
5182
South Asian (SAS)
AF:
0.621
AC:
2994
AN:
4820
European-Finnish (FIN)
AF:
0.658
AC:
6950
AN:
10560
Middle Eastern (MID)
AF:
0.568
AC:
167
AN:
294
European-Non Finnish (NFE)
AF:
0.703
AC:
47770
AN:
67976
Other (OTH)
AF:
0.610
AC:
1290
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1804
3607
5411
7214
9018
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
776
1552
2328
3104
3880
<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:
0.668
Hom.:
133839
Bravo
AF:
0.589
Asia WGS
AF:
0.575
AC:
2002
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
11
DANN
Benign
0.72
PhyloP100
0.58

Splicing

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

Publications

Other links and lift over

dbSNP: rs4698790; hg19: chr4-110727560; API