rs718226

Positions:

• chr16-50735652-A-G

Variant summary

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

The NR_184279.1(CYLD-AS1):​n.270-3292T>C 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 0.36 in 152,276 control chromosomes in the GnomAD database, including 10,496 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 0.36 (10447 hom., cov: 31)
  • Exomes 𝑓: 0.45 (49 hom.)
• Consequence: CYLD-AS1 NR_184279.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

Genes affected

CYLD-AS1 (HGNC:55352): (CYLD antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYLD-AS1	NR_184279.1	n.270-3292T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYLD-AS1	ENST00000563315.2	n.871-3292T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54601 AN: 151718 Hom.: 10452 Cov.: 31

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.368

GnomAD4 exome AF: 0.455 AC: 200 AN: 440 Hom.: 49 AF XY: 0.437 AC XY: 97 AN XY: 222

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.455

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.360 AC: 54613 AN: 151836 Hom.: 10447 Cov.: 31 AF XY: 0.357 AC XY: 26458 AN XY: 74202

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.364

Alfa AF: 0.371 Hom.: 1567

Bravo AF: 0.351

Asia WGS AF: 0.199 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718226; hg19: chr16-50769563;