rs2830208

chr21-26410783-C-Tchr21-26410783-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_135516.1(CYYR1-AS1):n.63+17086C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,080 control chromosomes in the GnomAD database, including 9,673 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 (9673 hom., cov: 32)
• Consequence: CYYR1-AS1 NR_135516.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

CYYR1-AS1 (HGNC:39560): (CYYR1 antisense RNA 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYYR1-AS1	NR_135516.1	n.63+17086C>T		intron_variant, non_coding_transcript_variant
CYYR1-AS1	NR_135515.1	n.186+4655C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYYR1-AS1	ENST00000357401.3	n.186+4655C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000429340.1	n.342+23001C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50979 AN: 151962 Hom.: 9664 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.335 AC: 51007 AN: 152080 Hom.: 9673 Cov.: 32 AF XY: 0.331 AC XY: 24644 AN XY: 74352

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.390

Alfa AF: 0.402 Hom.: 18157

Bravo AF: 0.329

Asia WGS AF: 0.291 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.37
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2830208; hg19: chr21-27783102;