rs961301

Variant names:

• chr21-26410720-A-G
• rs961301
• ENST00000357401.3:n.186+4592A>G

Variant summary

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

The ENST00000357401.3(CYYR1-AS1):​n.186+4592A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 152,092 control chromosomes in the GnomAD database, including 50,720 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 0.81 (50720 hom., cov: 31)
• Consequence: CYYR1-AS1 ENST00000357401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

Genes affected

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

ENSG00000232692 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYYR1-AS1	NR_135515.1	n.186+4592A>G		intron_variant	Intron 1 of 3
CYYR1-AS1	NR_135516.1	n.63+17023A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYYR1-AS1	ENST00000357401.3	n.186+4592A>G		intron_variant	Intron 1 of 3	2
CYYR1-AS1	ENST00000414486.5	n.63+17023A>G		intron_variant	Intron 1 of 3	2
ENSG00000232692	ENST00000421771.1	n.130+20455A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123754 AN: 151974 Hom.: 50689 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.814 AC: 123843 AN: 152092 Hom.: 50720 Cov.: 31 AF XY: 0.807 AC XY: 59950 AN XY: 74306

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.822

Alfa AF: 0.857 Hom.: 54929

Bravo AF: 0.829

Asia WGS AF: 0.655 AC: 2281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.62
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs961301; hg19: chr21-27783039;