rs219724

Variant names:

• chr21-26385622-C-T
• rs219724
• ENST00000429340.1:n.226-1379C>T

Variant summary

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

The ENST00000429340.1(CYYR1-AS1):​n.226-1379C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,114 control chromosomes in the GnomAD database, including 59,162 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 0.88 (59162 hom., cov: 30)
• Consequence: CYYR1-AS1 ENST00000429340.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.884 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	ENST00000429340.1	n.226-1379C>T		intron_variant	Intron 2 of 5	5
CYYR1-AS1	ENST00000717648.1	n.156-2102C>T		intron_variant	Intron 1 of 2
CYYR1-AS1	ENST00000723681.1	n.175-2102C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.881 AC: 133968 AN: 151996 Hom.: 59121 Cov.: 30

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.881 AC: 134067 AN: 152114 Hom.: 59162 Cov.: 30 AF XY: 0.882 AC XY: 65604 AN XY: 74372

African (AFR) AF: 0.873 AC: 36203 AN: 41486

American (AMR) AF: 0.865 AC: 13209 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3156 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4439 AN: 5170

South Asian (SAS) AF: 0.885 AC: 4252 AN: 4806

European-Finnish (FIN) AF: 0.893 AC: 9451 AN: 10580

Middle Eastern (MID) AF: 0.884 AC: 258 AN: 292

European-Non Finnish (NFE) AF: 0.890 AC: 60503 AN: 68008

Other (OTH) AF: 0.874 AC: 1844 AN: 2110

Alfa AF: 0.884 Hom.: 76440

Bravo AF: 0.876

Asia WGS AF: 0.864 AC: 3006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.21
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs219724; hg19: chr21-27757941;