rs2830191

Variant names:

• chr21-26370568-T-C
• rs2830191
• ENST00000717648.1:n.156-17156T>C

Variant summary

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

The ENST00000717648.1(CYYR1-AS1):​n.156-17156T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,158 control chromosomes in the GnomAD database, including 3,885 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 0.22 (3885 hom., cov: 32)
• Consequence: CYYR1-AS1 ENST00000717648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 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.156-17156T>C		intron_variant	Intron 1 of 2
CYYR1-AS1	ENST00000723681.1	n.174+12585T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32817 AN: 152040 Hom.: 3872 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.216 AC: 32869 AN: 152158 Hom.: 3885 Cov.: 32 AF XY: 0.215 AC XY: 16021 AN XY: 74376

African (AFR) AF: 0.300 AC: 12451 AN: 41478

American (AMR) AF: 0.207 AC: 3160 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3468

East Asian (EAS) AF: 0.0420 AC: 218 AN: 5186

South Asian (SAS) AF: 0.173 AC: 833 AN: 4820

European-Finnish (FIN) AF: 0.225 AC: 2382 AN: 10608

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12622 AN: 67992

Other (OTH) AF: 0.210 AC: 444 AN: 2112

Alfa AF: 0.194 Hom.: 1706

Bravo AF: 0.218

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.62
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs2830191; hg19: chr21-27742887;