Variant rs9264942 details in Genebe, Genetics Data Aggregator

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 151922 control chromosomes in the gnomAD Genomes database, including 9281 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 ( 9281 hom., cov: 32)

Consequence

LOC112267902
XR_926691.3 intron, non_coding_transcript

Scores

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -1.43

Links

LOC112267902 (HGNC:):

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

GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3 linkuse as main transcript	n.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.:

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

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 provided

literature only

OMIM

Dec 01, 2009

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

Cadd

Benign

5.9

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over