chr21-26361267-A-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYYR1-AS1	ENST00000717648.1	n.156-26457A>G		intron_variant	Intron 1 of 2
CYYR1-AS1	ENST00000723681.1	n.174+3284A>G		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs219683; hg19: chr21-27733586;