ENST00000357401.3:n.186+4655C>T

Variant names:

• chr21-26410783-C-T
• rs2830208
• ENST00000357401.3:n.186+4655C>T

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+4655C>T variant causes a intron 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 ENST00000357401.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 1 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=-0.89).
• 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 rank	MANE	Protein	UniProt
CYYR1-AS1	NR_135515.1	n.186+4655C>T		intron_variant	Intron 1 of 3
CYYR1-AS1	NR_135516.1	n.63+17086C>T		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+4655C>T		intron_variant	Intron 1 of 3	2
CYYR1-AS1	ENST00000414486.5	n.63+17086C>T		intron_variant	Intron 1 of 3	2
CYYR1-AS1	ENST00000421771.2	n.176+20518C>T		intron_variant	Intron 1 of 1	3

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

African (AFR) AF: 0.152 AC: 6287 AN: 41492

American (AMR) AF: 0.411 AC: 6275 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1517 AN: 3458

East Asian (EAS) AF: 0.277 AC: 1434 AN: 5174

South Asian (SAS) AF: 0.309 AC: 1488 AN: 4816

European-Finnish (FIN) AF: 0.374 AC: 3955 AN: 10564

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28794 AN: 67980

Other (OTH) AF: 0.390 AC: 823 AN: 2110

Alfa AF: 0.396 Hom.: 26542

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2830208; hg19: chr21-27783102;