rs219693

Variant names:

• chr21-26364673-A-G
• rs219693
• ENST00000717648.1:n.156-23051A>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.156-23051A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,024 control chromosomes in the GnomAD database, including 7,267 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 0.31 (7267 hom., cov: 32)
• Consequence: CYYR1-AS1 ENST00000717648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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.156-23051A>G		intron	N/A
	CYYR1-AS1	ENST00000723681.1		n.174+6690A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46352 AN: 151906 Hom.: 7252 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.305 AC: 46397 AN: 152024 Hom.: 7267 Cov.: 32 AF XY: 0.298 AC XY: 22154 AN XY: 74324

African (AFR) AF: 0.354 AC: 14653 AN: 41440

American (AMR) AF: 0.275 AC: 4203 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3468

East Asian (EAS) AF: 0.335 AC: 1729 AN: 5162

South Asian (SAS) AF: 0.221 AC: 1060 AN: 4806

European-Finnish (FIN) AF: 0.205 AC: 2171 AN: 10592

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20614 AN: 67970

Other (OTH) AF: 0.301 AC: 635 AN: 2108

Alfa AF: 0.298 Hom.: 11464

Bravo AF: 0.310

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs219693; hg19: chr21-27736992;