rs13050454

Variant names:

• chr21-26334004-G-A
• rs13050454
• ENST00000717648.1:n.156-53720G>A

Variant summary

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

The ENST00000717648.1(CYYR1-AS1):​n.156-53720G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,070 control chromosomes in the GnomAD database, including 9,838 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 0.34 (9838 hom., cov: 32)
• Consequence: CYYR1-AS1 ENST00000717648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 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.156-53720G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51646 AN: 151954 Hom.: 9833 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.340 AC: 51662 AN: 152070 Hom.: 9838 Cov.: 32 AF XY: 0.345 AC XY: 25618 AN XY: 74314

African (AFR) AF: 0.151 AC: 6283 AN: 41492

American (AMR) AF: 0.382 AC: 5836 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1503 AN: 3466

East Asian (EAS) AF: 0.367 AC: 1889 AN: 5150

South Asian (SAS) AF: 0.418 AC: 2017 AN: 4824

European-Finnish (FIN) AF: 0.472 AC: 4994 AN: 10576

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

European-Non Finnish (NFE) AF: 0.410 AC: 27871 AN: 67980

Other (OTH) AF: 0.362 AC: 763 AN: 2106

Alfa AF: 0.386 Hom.: 36443

Bravo AF: 0.324

Asia WGS AF: 0.396 AC: 1377 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	2.4
DANN	Benign	0.62
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs13050454; hg19: chr21-27706323;