21-36122680-A-G

Variant names:

• chr21-36122680-A-G
• rs4816519
• ENST00000718361.1:n.590+9916T>C

Variant summary

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

The ENST00000718361.1(CBR3-AS1):​n.590+9916T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,060 control chromosomes in the GnomAD database, including 54,709 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 0.85 (54709 hom., cov: 31)
• Consequence: CBR3-AS1 ENST00000718361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 9 publications found

Genes affected

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

ENSG00000295923 (HGNC:):

CBR1-AS1 (HGNC:55777): (CBR1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CBR1-AS1	NR_040084.1	n.154+3807T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CBR3-AS1	ENST00000718361.1	n.590+9916T>C		intron_variant	Intron 2 of 2
CBR3-AS1	ENST00000718362.1	n.793+9916T>C		intron_variant	Intron 2 of 2
ENSG00000295923	ENST00000733949.1	n.168+402T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128770 AN: 151942 Hom.: 54664 Cov.: 31

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.847 AC: 128870 AN: 152060 Hom.: 54709 Cov.: 31 AF XY: 0.843 AC XY: 62683 AN XY: 74324

African (AFR) AF: 0.821 AC: 34038 AN: 41482

American (AMR) AF: 0.827 AC: 12609 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3114 AN: 3472

East Asian (EAS) AF: 0.834 AC: 4316 AN: 5172

South Asian (SAS) AF: 0.828 AC: 3989 AN: 4820

European-Finnish (FIN) AF: 0.801 AC: 8451 AN: 10556

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59558 AN: 68000

Other (OTH) AF: 0.855 AC: 1805 AN: 2110

Alfa AF: 0.865 Hom.: 35936

Bravo AF: 0.850

Asia WGS AF: 0.793 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.16
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4816519; hg19: chr21-37494978;