rs9264942
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_926691.3(LOC112267902):n.964+175A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,040 control chromosomes in the GnomAD database, including 9,279 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: 𝑓 0.34 ( 9279 hom., cov: 32)
Consequence
LOC112267902
XR_926691.3 intron
XR_926691.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.43
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=-1.0).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LOC112267902 | XR_926691.3 | n.964+175A>G | intron_variant | Intron 3 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes AF: 0.344 AC: 52288AN: 151922Hom.: 9281 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
52288
AN:
151922
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.344 AC: 52309AN: 152040Hom.: 9279 Cov.: 32 AF XY: 0.343 AC XY: 25522AN XY: 74318 show subpopulations
GnomAD4 genome
AF:
AC:
52309
AN:
152040
Hom.:
Cov.:
32
AF XY:
AC XY:
25522
AN XY:
74318
Gnomad4 AFR
AF:
AC:
0.303393
AN:
0.303393
Gnomad4 AMR
AF:
AC:
0.30986
AN:
0.30986
Gnomad4 ASJ
AF:
AC:
0.580403
AN:
0.580403
Gnomad4 EAS
AF:
AC:
0.393951
AN:
0.393951
Gnomad4 SAS
AF:
AC:
0.507877
AN:
0.507877
Gnomad4 FIN
AF:
AC:
0.271113
AN:
0.271113
Gnomad4 NFE
AF:
AC:
0.358636
AN:
0.358636
Gnomad4 OTH
AF:
AC:
0.366604
AN:
0.366604
Heterozygous variant carriers
0
1763
3527
5290
7054
8817
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
516
1032
1548
2064
2580
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1461
AN:
3478
ClinVar
Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
HIV-1 VIREMIA, SUSCEPTIBILITY TO Other:1
Dec 01, 2009
OMIM
Significance:risk factor
Review Status:no assertion criteria provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at