rs7205423

Positions:

• chr16-50735351-C-G
• chr16-50735351-C-T

Variant summary

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

The NR_184279.1(CYLD-AS1):​n.270-2991G>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 0.577 in 151,920 control chromosomes in the GnomAD database, including 26,368 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 0.58 (26368 hom., cov: 31)
• Consequence: CYLD-AS1 NR_184279.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYLD-AS1	NR_184279.1	n.270-2991G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYLD-AS1	ENST00000563315.2	n.871-2991G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87503 AN: 151802 Hom.: 26314 Cov.: 31

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.577 AC: 87610 AN: 151920 Hom.: 26368 Cov.: 31 AF XY: 0.572 AC XY: 42493 AN XY: 74232

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.537

Alfa AF: 0.388 Hom.: 952

Bravo AF: 0.576

Asia WGS AF: 0.385 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7205423; hg19: chr16-50769262;