21-26304273-T-G

Variant names:

• chr21-26304273-T-G
• rs2830165
• ENST00000717648.1:n.155+25341T>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.155+25341T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,986 control chromosomes in the GnomAD database, including 9,602 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 0.33 (9602 hom., cov: 32)
• Consequence: CYYR1-AS1 ENST00000717648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYYR1-AS1	ENST00000717648.1		n.155+25341T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50086 AN: 151866 Hom.: 9596 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.330 AC: 50100 AN: 151986 Hom.: 9602 Cov.: 32 AF XY: 0.333 AC XY: 24759 AN XY: 74272

African (AFR) AF: 0.127 AC: 5282 AN: 41516

American (AMR) AF: 0.379 AC: 5782 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1499 AN: 3472

East Asian (EAS) AF: 0.277 AC: 1429 AN: 5168

South Asian (SAS) AF: 0.406 AC: 1954 AN: 4816

European-Finnish (FIN) AF: 0.468 AC: 4946 AN: 10574

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.412 AC: 27968 AN: 67870

Other (OTH) AF: 0.348 AC: 734 AN: 2110

Alfa AF: 0.389 Hom.: 49931

Bravo AF: 0.314

Asia WGS AF: 0.337 AC: 1173 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.71
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2830165; hg19: chr21-27676592;