rs2212922

Variant names:

• chr21-36126057-G-A
• rs2212922
• ENST00000718361.1:n.590+6539C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-36126057-G-A
• chr21-36126057-G-C

Variant summary

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

The NR_040084.1(CBR1-AS1):​n.154+430C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,002 control chromosomes in the GnomAD database, including 13,063 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 0.41 (13063 hom., cov: 32)
• Consequence: CBR1-AS1 NR_040084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 13 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_040084.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CBR1-AS1	NR_040084.1		n.154+430C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CBR3-AS1	ENST00000718361.1		n.590+6539C>T		intron	N/A
	CBR3-AS1	ENST00000718362.1		n.793+6539C>T		intron	N/A
	ENSG00000295923	ENST00000733949.1		n.70-2877C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61910 AN: 151884 Hom.: 13051 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.408 AC: 61973 AN: 152002 Hom.: 13063 Cov.: 32 AF XY: 0.407 AC XY: 30264 AN XY: 74308

African (AFR) AF: 0.305 AC: 12658 AN: 41460

American (AMR) AF: 0.469 AC: 7164 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1587 AN: 3472

East Asian (EAS) AF: 0.444 AC: 2290 AN: 5156

South Asian (SAS) AF: 0.313 AC: 1508 AN: 4814

European-Finnish (FIN) AF: 0.415 AC: 4388 AN: 10562

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31060 AN: 67958

Other (OTH) AF: 0.437 AC: 921 AN: 2106

Alfa AF: 0.448 Hom.: 26227

Bravo AF: 0.411

Asia WGS AF: 0.356 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.78
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2212922; hg19: chr21-37498355;