chr21-26305471-G-A

Variant names:

• chr21-26305471-G-A
• rs461626
• ENST00000717648.1:n.155+26539G>A

Variant summary

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

The ENST00000717648.1(CYYR1-AS1):​n.155+26539G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,206 control chromosomes in the GnomAD database, including 54,374 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 0.84 (54374 hom., cov: 32)
• Consequence: CYYR1-AS1 ENST00000717648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.879 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYYR1-AS1	ENST00000717648.1		n.155+26539G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128413 AN: 152088 Hom.: 54323 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.844 AC: 128520 AN: 152206 Hom.: 54374 Cov.: 32 AF XY: 0.847 AC XY: 63049 AN XY: 74402

African (AFR) AF: 0.828 AC: 34391 AN: 41540

American (AMR) AF: 0.892 AC: 13617 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3164 AN: 3470

East Asian (EAS) AF: 0.725 AC: 3754 AN: 5178

South Asian (SAS) AF: 0.887 AC: 4283 AN: 4828

European-Finnish (FIN) AF: 0.875 AC: 9266 AN: 10592

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57144 AN: 68006

Other (OTH) AF: 0.854 AC: 1805 AN: 2114

Alfa AF: 0.846 Hom.: 15490

Bravo AF: 0.844

Asia WGS AF: 0.836 AC: 2908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.48
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs461626; hg19: chr21-27677790;