rs961301

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000357401.3. 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
	CYYR1-AS1	NR_135515.1		n.186+4592A>G		intron	N/A
	CYYR1-AS1	NR_135516.1		n.63+17023A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYYR1-AS1	ENST00000357401.3	TSL:2	n.186+4592A>G		intron	N/A
	CYYR1-AS1	ENST00000414486.5	TSL:2	n.63+17023A>G		intron	N/A
	CYYR1-AS1	ENST00000421771.2	TSL:3	n.176+20455A>G		intron	N/A

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

African (AFR) AF: 0.783 AC: 32485 AN: 41484

American (AMR) AF: 0.887 AC: 13549 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3032 AN: 3470

East Asian (EAS) AF: 0.581 AC: 3000 AN: 5160

South Asian (SAS) AF: 0.743 AC: 3579 AN: 4818

European-Finnish (FIN) AF: 0.697 AC: 7355 AN: 10558

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58035 AN: 68000

Other (OTH) AF: 0.822 AC: 1740 AN: 2116

Alfa AF: 0.850 Hom.: 84060

Bravo AF: 0.829

Asia WGS AF: 0.655 AC: 2281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.62
DANN	Benign	0.41
PhyloP100		-0.41

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs961301;

hg19: chr21-27783039;