rs10483032

chr21-36140267-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001236.4(CBR3):c.397+2335A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 151,938 control chromosomes in the GnomAD database, including 61,316 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 0.90 (61316 hom., cov: 29)
• Consequence: CBR3 NM_001236.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CBR3	NM_001236.4	c.397+2335A>G		intron_variant		ENST00000290354.6
CBR3-AS1	NR_038893.1	n.192+5989T>C		intron_variant, non_coding_transcript_variant
CBR3	XM_011529772.3	c.398-1657A>G		intron_variant
CBR3-AS1	NR_038892.1	n.192+5989T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CBR3	ENST00000290354.6	c.397+2335A>G		intron_variant		1	NM_001236.4	P1
CBR3-AS1	ENST00000624080.1	n.149-6794T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136138 AN: 151820 Hom.: 61264 Cov.: 29

Gnomad AFR AF: 0.977

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.899

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.897 AC: 136247 AN: 151938 Hom.: 61316 Cov.: 29 AF XY: 0.891 AC XY: 66175 AN XY: 74240

Gnomad4 AFR AF: 0.977

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.895

Alfa AF: 0.883 Hom.: 50370

Bravo AF: 0.905

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.032
Dann	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483032; hg19: chr21-37512565;