21-36134468-C-T

Variant names:

• chr21-36134468-C-T
• rs2239566
• ENST00000453159.7:n.271-1394G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000453159.7(CBR3-AS1):​n.271-1394G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,228 control chromosomes in the GnomAD database, including 52,479 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 0.83 (52479 hom., cov: 33)
• Consequence: CBR3-AS1 ENST00000453159.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CBR3-AS1	NR_038892.1	n.193-707G>A		intron_variant	Intron 2 of 3
CBR3-AS1	NR_038893.1	n.193-1394G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CBR3-AS1	ENST00000453159.7	n.271-1394G>A		intron_variant	Intron 2 of 2	1
CBR3-AS1	ENST00000413862.8	n.245-707G>A		intron_variant	Intron 2 of 3	5
CBR3-AS1	ENST00000608622.6	n.312-1394G>A		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126103 AN: 152110 Hom.: 52445 Cov.: 33

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.829 AC: 126190 AN: 152228 Hom.: 52479 Cov.: 33 AF XY: 0.825 AC XY: 61380 AN XY: 74408

African (AFR) AF: 0.765 AC: 31756 AN: 41512

American (AMR) AF: 0.814 AC: 12444 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2853 AN: 3468

East Asian (EAS) AF: 0.845 AC: 4372 AN: 5172

South Asian (SAS) AF: 0.851 AC: 4113 AN: 4832

European-Finnish (FIN) AF: 0.798 AC: 8456 AN: 10592

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59458 AN: 68034

Other (OTH) AF: 0.842 AC: 1781 AN: 2116

Alfa AF: 0.858 Hom.: 65432

Bravo AF: 0.829

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.76
DANN	Benign	0.80
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2239566; hg19: chr21-37506766;