21-26385450-A-C

Variant names:

• chr21-26385450-A-C
• rs219722
• ENST00000429340.1:n.226-1551A>C

Variant summary

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

The ENST00000717648.1(CYYR1-AS1):​n.156-2274A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 151,330 control chromosomes in the GnomAD database, including 59,486 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 (59486 hom., cov: 30)
• Consequence: CYYR1-AS1 ENST00000717648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494
• Publications: 2 publications found

Genes affected

CYYR1-AS1 (HGNC:39560): (CYYR1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717648.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYYR1-AS1	ENST00000429340.1	TSL:5	n.226-1551A>C		intron	N/A
	CYYR1-AS1	ENST00000717648.1		n.156-2274A>C		intron	N/A
	CYYR1-AS1	ENST00000723681.1		n.175-2274A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134003 AN: 151218 Hom.: 59459 Cov.: 30

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.886 AC: 134083 AN: 151330 Hom.: 59486 Cov.: 30 AF XY: 0.886 AC XY: 65570 AN XY: 73988

African (AFR) AF: 0.868 AC: 35834 AN: 41286

American (AMR) AF: 0.874 AC: 13293 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 3197 AN: 3464

East Asian (EAS) AF: 0.858 AC: 4416 AN: 5146

South Asian (SAS) AF: 0.886 AC: 4246 AN: 4792

European-Finnish (FIN) AF: 0.898 AC: 9209 AN: 10256

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 60980 AN: 67860

Other (OTH) AF: 0.883 AC: 1858 AN: 2104

Alfa AF: 0.896 Hom.: 7584

Bravo AF: 0.882

Asia WGS AF: 0.861 AC: 2983 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.63
PhyloP100		0.49

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs219722;

hg19: chr21-27757769;