GeneBe

XR_007058768.1:n.515+705A>G

Variant names:

Variant summary

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

The XR_007058768.1(LOC124900975):​n.515+705A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,124 control chromosomes in the GnomAD database, including 6,173 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 0.25 ( 6173 hom., cov: 32)

Consequence

LOC124900975
XR_007058768.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

Publications

1 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=-0.77).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC124900975XR_007058768.1 linkn.515+705A>G intron_variant Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.250
AC:
37944
AN:
152006
Hom.:
6156
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.448
Gnomad AMI
AF:
0.0570
Gnomad AMR
AF:
0.213
Gnomad ASJ
AF:
0.181
Gnomad EAS
AF:
0.464
Gnomad SAS
AF:
0.263
Gnomad FIN
AF:
0.135
Gnomad MID
AF:
0.213
Gnomad NFE
AF:
0.144
Gnomad OTH
AF:
0.254
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.250
AC:
38000
AN:
152124
Hom.:
6173
Cov.:
32
AF XY:
0.251
AC XY:
18638
AN XY:
74374
show subpopulations
African (AFR)
AF:
0.449
AC:
18604
AN:
41468
American (AMR)
AF:
0.213
AC:
3257
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.181
AC:
630
AN:
3472
East Asian (EAS)
AF:
0.464
AC:
2394
AN:
5164
South Asian (SAS)
AF:
0.263
AC:
1265
AN:
4818
European-Finnish (FIN)
AF:
0.135
AC:
1430
AN:
10616
Middle Eastern (MID)
AF:
0.199
AC:
58
AN:
292
European-Non Finnish (NFE)
AF:
0.144
AC:
9771
AN:
67980
Other (OTH)
AF:
0.255
AC:
539
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1318
2635
3953
5270
6588
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
372
744
1116
1488
1860
<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:
0.210
Hom.:
600
Bravo
AF:
0.266
Asia WGS
AF:
0.345
AC:
1198
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
4.3
DANN
Benign
0.78
PhyloP100
0.35

Splicing

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

Publications

Other links and lift over

dbSNP: rs171740; hg19: chr5-53009957; API