rs468345

Variant names:

• chr21-26288563-A-C
• rs468345
• ENST00000717648.1:n.155+9631A>C

Your query was ambiguous. Multiple possible variants found:

• chr21-26288563-A-C
• chr21-26288563-A-T

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+9631A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,002 control chromosomes in the GnomAD database, including 29,990 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 0.62 (29990 hom., cov: 32)
• Consequence: CYYR1-AS1 ENST00000717648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.726 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.155+9631A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94414 AN: 151884 Hom.: 29977 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.622 AC: 94474 AN: 152002 Hom.: 29990 Cov.: 32 AF XY: 0.625 AC XY: 46407 AN XY: 74270

African (AFR) AF: 0.491 AC: 20337 AN: 41434

American (AMR) AF: 0.668 AC: 10194 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2659 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3517 AN: 5174

South Asian (SAS) AF: 0.746 AC: 3595 AN: 4818

European-Finnish (FIN) AF: 0.643 AC: 6780 AN: 10540

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45108 AN: 67986

Other (OTH) AF: 0.649 AC: 1373 AN: 2114

Alfa AF: 0.646 Hom.: 67672

Bravo AF: 0.620

Asia WGS AF: 0.699 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.76
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs468345; hg19: chr21-27660882;