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GeneBe

rs9264942

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_926691.3(LOC112267902):n.964+175A>G variant causes a intron, non coding transcript 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, non_coding_transcript

Scores

2

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -1.43
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
LOC112267902XR_926691.3 linkuse as main transcriptn.964+175A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.344
AC:
52288
AN:
151922
Hom.:
9281
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.303
Gnomad AMI
AF:
0.407
Gnomad AMR
AF:
0.310
Gnomad ASJ
AF:
0.580
Gnomad EAS
AF:
0.394
Gnomad SAS
AF:
0.508
Gnomad FIN
AF:
0.271
Gnomad MID
AF:
0.399
Gnomad NFE
AF:
0.359
Gnomad OTH
AF:
0.369
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.344
AC:
52309
AN:
152040
Hom.:
9279
Cov.:
32
AF XY:
0.343
AC XY:
25522
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.303
Gnomad4 AMR
AF:
0.310
Gnomad4 ASJ
AF:
0.580
Gnomad4 EAS
AF:
0.394
Gnomad4 SAS
AF:
0.508
Gnomad4 FIN
AF:
0.271
Gnomad4 NFE
AF:
0.359
Gnomad4 OTH
AF:
0.367
Alfa
AF:
0.369
Hom.:
19478
Bravo
AF:
0.344
Asia WGS
AF:
0.420
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
risk factor, no assertion criteria providedliterature onlyOMIMDec 01, 2009- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
4.4
Dann
Benign
0.71

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9264942; hg19: chr6-31274380; API