21-36134867-A-T

Variant summary

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

The NR_038893.1(CBR3-AS1):n.193-1793T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 307,058 control chromosomes in the GnomAD database, including 119,138 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 0.89 (59916 hom., cov: 32)
  • Exomes 𝑓: 0.87 (59222 hom.)
• Consequence: CBR3-AS1 NR_038893.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.24

Genes affected

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CBR3-AS1	NR_038893.1	n.193-1793T>A		intron_variant, non_coding_transcript_variant
CBR3-AS1	NR_038892.1	n.193-1106T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CBR3-AS1	ENST00000624080.1	n.149-1394T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134810 AN: 152106 Hom.: 59872 Cov.: 32

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.893

GnomAD4 exome AF: 0.874 AC: 135256 AN: 154836 Hom.: 59222 Cov.: 2 AF XY: 0.876 AC XY: 67573 AN XY: 77146

Gnomad4 AFR exome AF: 0.943

Gnomad4 AMR exome AF: 0.836

Gnomad4 ASJ exome AF: 0.909

Gnomad4 EAS exome AF: 0.835

Gnomad4 SAS exome AF: 0.867

Gnomad4 FIN exome AF: 0.785

Gnomad4 NFE exome AF: 0.884

Gnomad4 OTH exome AF: 0.878

GnomAD4 genome AF: 0.886 AC: 134909 AN: 152222 Hom.: 59916 Cov.: 32 AF XY: 0.881 AC XY: 65565 AN XY: 74404

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.903

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.888

Alfa AF: 0.825 Hom.: 2511

Bravo AF: 0.893

Asia WGS AF: 0.830 AC: 2886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.13
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8132243; hg19: chr21-37507165;