Genetic Variant ENST00000453159.7:n.271-1793T>G (chr21-36134867-A-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000453159.7(CBR3-AS1):n.271-1793T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CBR3-AS1
ENST00000453159.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.24

Publications

6 publications found

Variant links:

Genes affected

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

CBR3-AS1 links:

CBR3 (HGNC:1549): (carbonyl reductase 3) Carbonyl reductase 3 catalyzes the reduction of a large number of biologically and pharmacologically active carbonyl compounds to their corresponding alcohols. The enzyme is classified as a monomeric NADPH-dependent oxidoreductase. CBR3 contains three exons spanning 11.2 kilobases and is closely linked to another carbonyl reductase gene - CBR1. [provided by RefSeq, Jul 2008]

CBR3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453159.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CBR3-AS1	NR_038892.1		n.193-1106T>G	intron	N/A
CBR3-AS1	NR_038893.1		n.193-1793T>G	intron	N/A
CBR3	NM_001236.4	MANE Select	c.-326A>C	upstream_gene	N/A	NP_001227.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
CBR3-AS1	ENST00000453159.7	TSL:1	n.271-1793T>G	intron	N/A
CBR3-AS1	ENST00000625189.3	TSL:5	n.7T>G	non_coding_transcript_exon	Exon 1 of 2
CBR3-AS1	ENST00000661388.1		n.553T>G	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

155106

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

77288

African (AFR)

AF:

0.00

AC:

AN:

5320

American (AMR)

AF:

0.00

AC:

AN:

4604

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6562

East Asian (EAS)

AF:

0.00

AC:

AN:

14000

South Asian (SAS)

AF:

0.00

AC:

AN:

2336

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10876

Middle Eastern (MID)

AF:

0.00

AC:

AN:

828

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

99462

Other (OTH)

AF:

0.00

AC:

AN:

11118

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

2511

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.13

(source)

DANN

Benign

0.21

PhyloP100

-4.2

PromoterAI

0.015

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over