21-26344335-C-T

Variant names:

• chr21-26344335-C-T
• rs9975851
• ENST00000717648.1:n.156-43389C>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.156-43389C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,748 control chromosomes in the GnomAD database, including 23,672 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 0.55 (23672 hom., cov: 32)
• Consequence: CYYR1-AS1 ENST00000717648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYYR1-AS1	ENST00000717648.1		n.156-43389C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84019 AN: 151628 Hom.: 23654 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.554 AC: 84073 AN: 151748 Hom.: 23672 Cov.: 32 AF XY: 0.558 AC XY: 41409 AN XY: 74148

African (AFR) AF: 0.473 AC: 19575 AN: 41400

American (AMR) AF: 0.519 AC: 7892 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1857 AN: 3466

East Asian (EAS) AF: 0.781 AC: 4026 AN: 5154

South Asian (SAS) AF: 0.627 AC: 3022 AN: 4818

European-Finnish (FIN) AF: 0.628 AC: 6639 AN: 10564

Middle Eastern (MID) AF: 0.507 AC: 147 AN: 290

European-Non Finnish (NFE) AF: 0.579 AC: 39252 AN: 67828

Other (OTH) AF: 0.554 AC: 1168 AN: 2108

Alfa AF: 0.527 Hom.: 7862

Bravo AF: 0.541

Asia WGS AF: 0.699 AC: 2421 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.1
DANN	Benign	0.74
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs9975851; hg19: chr21-27716654;