21-26433872-A-G

Variant names:

• chr21-26433872-A-G
• rs219664
• ENST00000357401.3:n.186+27744A>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+27744A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,194 control chromosomes in the GnomAD database, including 59,489 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 0.88 (59489 hom., cov: 31)
• Consequence: CYYR1-AS1 ENST00000357401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13
• Publications: 2 publications found

Genes affected

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

ENSG00000294485 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 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+27744A>G		intron	N/A
	CYYR1-AS1	NR_135516.1		n.63+40175A>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+27744A>G		intron	N/A
	CYYR1-AS1	ENST00000414486.5	TSL:2	n.63+40175A>G		intron	N/A
	CYYR1-AS1	ENST00000421771.2	TSL:3	n.177-36879A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134093 AN: 152076 Hom.: 59454 Cov.: 31

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.882 AC: 134182 AN: 152194 Hom.: 59489 Cov.: 31 AF XY: 0.876 AC XY: 65182 AN XY: 74384

African (AFR) AF: 0.946 AC: 39294 AN: 41542

American (AMR) AF: 0.896 AC: 13705 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3022 AN: 3470

East Asian (EAS) AF: 0.626 AC: 3231 AN: 5162

South Asian (SAS) AF: 0.782 AC: 3764 AN: 4812

European-Finnish (FIN) AF: 0.800 AC: 8465 AN: 10576

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

European-Non Finnish (NFE) AF: 0.878 AC: 59688 AN: 68016

Other (OTH) AF: 0.879 AC: 1860 AN: 2116

Alfa AF: 0.870 Hom.: 7611

Bravo AF: 0.892

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.33
PhyloP100		2.1

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: rs219664;

hg19: chr21-27806191;