Variant rs8132243 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_038893.1(CBR3-AS1):n.193-1793T>A 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 0.88 in 307,058 control chromosomes in the GnomAD database, including 119,138 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 0.89 ( 59916 hom., cov: 32)

Exomes 𝑓: 0.87 ( 59222 hom. )

Consequence

CBR3-AS1
NR_038893.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.24

Variant links:

Genes affected

CBR3-AS1 (HGNC:43664): (CBR3 antisense RNA 1)

CBR3-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CBR3-AS1	NR_038893.1 linkuse as main transcript	n.193-1793T>A		intron_variant, non_coding_transcript_variant
CBR3-AS1	NR_038892.1 linkuse as main transcript	n.193-1106T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CBR3-AS1	ENST00000624080.1 linkuse as main transcript	n.149-1394T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.886

AC:

134810

AN:

152106

Hom.:

59872

Cov.:

show subpopulations

Gnomad AFR

AF:

0.943

Gnomad AMI

AF:

0.818

Gnomad AMR

AF:

0.843

Gnomad ASJ

AF:

0.903

Gnomad EAS

AF:

0.846

Gnomad SAS

AF:

0.867

Gnomad FIN

AF:

0.797

Gnomad MID

AF:

0.880

Gnomad NFE

AF:

0.880

Gnomad OTH

AF:

0.893

GnomAD4 exome

AF:

0.874

AC:

135256

AN:

154836

Hom.:

59222

Cov.:

AF XY:

0.876

AC XY:

67573

AN XY:

77146

show subpopulations

Gnomad4 AFR exome

AF:

0.943

Gnomad4 AMR exome

AF:

0.836

Gnomad4 ASJ exome

AF:

0.909

Gnomad4 EAS exome

AF:

0.835

Gnomad4 SAS exome

AF:

0.867

Gnomad4 FIN exome

AF:

0.785

Gnomad4 NFE exome

AF:

0.884

Gnomad4 OTH exome

AF:

0.878

GnomAD4 genome

AF:

0.886

AC:

134909

AN:

152222

Hom.:

59916

Cov.:

AF XY:

0.881

AC XY:

65565

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.943

Gnomad4 AMR

AF:

0.843

Gnomad4 ASJ

AF:

0.903

Gnomad4 EAS

AF:

0.846

Gnomad4 SAS

AF:

0.867

Gnomad4 FIN

AF:

0.797

Gnomad4 NFE

AF:

0.880

Gnomad4 OTH

AF:

0.888

Alfa

AF:

0.825

Hom.:

2511

Bravo

AF:

0.893

Asia WGS

AF:

0.830

AC:

2886

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.13

DANN

Benign

0.56

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

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over