chr21-36134468-C-T

Position:

• chr21-36134468-C-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.193-1394G>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 0.829 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 NR_038893.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587

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=-0.83).
• 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/exons	MANE	UniProt
CBR3-AS1	NR_038893.1	n.193-1394G>A		intron_variant, non_coding_transcript_variant
CBR3-AS1	NR_038892.1	n.193-707G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CBR3-AS1	ENST00000624080.1	n.149-995G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.814

Gnomad4 ASJ AF: 0.823

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.851

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.842

Alfa AF: 0.862 Hom.: 49010

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2239566; hg19: chr21-37506766;