rs219664

chr21-26433872-A-Gchr21-26433872-A-C

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+40175A>G 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 0.882 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 NR_135516.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYYR1-AS1	NR_135516.1	n.63+40175A>G		intron_variant, non_coding_transcript_variant
LOC105372758	XR_937627.3	n.328+1695T>C		intron_variant, non_coding_transcript_variant
CYYR1-AS1	NR_135515.1	n.186+27744A>G		intron_variant, non_coding_transcript_variant
LOC105372758	XR_937624.3	n.329-1084T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYYR1-AS1	ENST00000357401.3	n.186+27744A>G		intron_variant, non_coding_transcript_variant		2
	ENST00000429340.1	n.343-36688A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.879

Alfa AF: 0.867 Hom.: 7270

Bravo AF: 0.892

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.7
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs219664; hg19: chr21-27806191;