rs219683

Variant names:

• chr21-26361267-A-G
• rs219683
• ENST00000717648.1:n.156-26457A>G

Variant summary

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

The ENST00000717648.1(CYYR1-AS1):​n.156-26457A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,156 control chromosomes in the GnomAD database, including 2,189 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 0.16 (2189 hom., cov: 32)
• Consequence: CYYR1-AS1 ENST00000717648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.858
• Publications: 0 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 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	ENST00000717648.1		n.156-26457A>G		intron	N/A
	CYYR1-AS1	ENST00000723681.1		n.174+3284A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25032 AN: 152038 Hom.: 2185 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0959

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.165 AC: 25045 AN: 152156 Hom.: 2189 Cov.: 32 AF XY: 0.162 AC XY: 12040 AN XY: 74374

African (AFR) AF: 0.181 AC: 7520 AN: 41526

American (AMR) AF: 0.116 AC: 1772 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0959 AC: 333 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1560 AN: 5164

South Asian (SAS) AF: 0.166 AC: 799 AN: 4824

European-Finnish (FIN) AF: 0.127 AC: 1347 AN: 10584

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.166 AC: 11257 AN: 67988

Other (OTH) AF: 0.154 AC: 325 AN: 2110

Alfa AF: 0.160 Hom.: 2758

Bravo AF: 0.164

Asia WGS AF: 0.199 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.5
DANN	Benign	0.57
PhyloP100		0.86

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: rs219683;

hg19: chr21-27733586;