16-50741834-T-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.78-430A>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 0.348 in 152,036 control chromosomes in the GnomAD database, including 9,958 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 0.35 (9958 hom., cov: 33)
• Consequence: CYLD-AS1 NR_184279.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600

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=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYLD-AS1	NR_184279.1	n.78-430A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYLD-AS1	ENST00000563315.2	n.146-430A>C		intron_variant, non_coding_transcript_variant		5
CYLD-AS1	ENST00000567728.2	n.90-430A>C		intron_variant, non_coding_transcript_variant		3
CYLD-AS1	ENST00000688175.1	n.78-430A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52859 AN: 151916 Hom.: 9960 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.348 AC: 52887 AN: 152036 Hom.: 9958 Cov.: 33 AF XY: 0.345 AC XY: 25621 AN XY: 74314

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.353

Alfa AF: 0.253 Hom.: 629

Bravo AF: 0.339

Asia WGS AF: 0.198 AC: 685 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	3.0
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs751919; hg19: chr16-50775745;