rs4817775

Positions:

• chr21-36112764-A-C
• chr21-36112764-A-G

Variant summary

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

The NR_040084.1(CBR1-AS1):​n.154+13723T>G 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 0.483 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: CBR1-AS1 NR_040084.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CBR1-AS1	NR_040084.1	n.154+13723T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CBR1-AS1	ENST00000535199.5	n.154+13723T>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.455

Alfa AF: 0.435 Hom.: 19524

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4817775; hg19: chr21-37485062;