rs8056611

chr16-50733736-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.270-1376T>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 0.553 in 151,928 control chromosomes in the GnomAD database, including 24,085 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 0.55 (24082 hom., cov: 30)
  • Exomes 𝑓: 0.54 (3 hom.)
• Consequence: CYLD-AS1 NR_184279.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYLD-AS1	NR_184279.1	n.270-1376T>C		intron_variant, non_coding_transcript_variant
CYLD-AS1	NR_184278.1	n.803-1376T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYLD-AS1	ENST00000563315.2	n.871-1376T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83857 AN: 151788 Hom.: 24029 Cov.: 30

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.520

GnomAD4 exome AF: 0.542 AC: 13 AN: 24 Hom.: 3 Cov.: 0 AF XY: 0.550 AC XY: 11 AN XY: 20

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.550

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.553 AC: 83967 AN: 151904 Hom.: 24082 Cov.: 30 AF XY: 0.549 AC XY: 40776 AN XY: 74270

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.518

Alfa AF: 0.522 Hom.: 5756

Bravo AF: 0.553

Asia WGS AF: 0.393 AC: 1368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.9
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8056611; hg19: chr16-50767647;