chr21-36112764-A-C

Variant names:

• chr21-36112764-A-C
• rs4817775
• ENST00000718361.1:n.591-14505T>G

Variant summary

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

The ENST00000718361.1(CBR3-AS1):​n.591-14505T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,872 control chromosomes in the GnomAD database, including 18,513 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 0.48 (18513 hom., cov: 32)
• Consequence: CBR3-AS1 ENST00000718361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 27 publications found

Genes affected

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

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CBR1-AS1	NR_040084.1	n.154+13723T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CBR3-AS1	ENST00000718361.1	n.591-14505T>G		intron_variant	Intron 2 of 2
CBR3-AS1	ENST00000718362.1	n.794-14505T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73237 AN: 151754 Hom.: 18492 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.483 AC: 73302 AN: 151872 Hom.: 18513 Cov.: 32 AF XY: 0.480 AC XY: 35598 AN XY: 74192

African (AFR) AF: 0.643 AC: 26636 AN: 41410

American (AMR) AF: 0.374 AC: 5715 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2038 AN: 5166

South Asian (SAS) AF: 0.515 AC: 2476 AN: 4808

European-Finnish (FIN) AF: 0.408 AC: 4300 AN: 10534

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28916 AN: 67910

Other (OTH) AF: 0.455 AC: 960 AN: 2110

Alfa AF: 0.439 Hom.: 51746

Bravo AF: 0.484

Asia WGS AF: 0.455 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.35
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4817775; hg19: chr21-37485062;