NR_184273.1:n.1667G>C

Variant names:

• chr16-50735351-C-G
• rs7205423
• NR_184273.1:n.1667G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_184273.1(CYLD-AS1):​n.1667G>C variant causes a non coding transcript exon 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_184273.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_184273.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYLD-AS1	NR_184273.1		n.1667G>C		non_coding_transcript_exon	Exon 3 of 3
	CYLD-AS1	NR_184274.1		n.1744G>C		non_coding_transcript_exon	Exon 4 of 4
	CYLD-AS1	NR_184275.1		n.1817G>C		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYLD-AS1	ENST00000563315.2	TSL:5	n.871-2991G>C		intron	N/A

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

African (AFR) AF: 0.738 AC: 30564 AN: 41432

American (AMR) AF: 0.494 AC: 7533 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2316 AN: 3468

East Asian (EAS) AF: 0.229 AC: 1183 AN: 5156

South Asian (SAS) AF: 0.469 AC: 2263 AN: 4824

European-Finnish (FIN) AF: 0.541 AC: 5705 AN: 10544

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36214 AN: 67922

Other (OTH) AF: 0.537 AC: 1134 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.1
DANN	Benign	0.54
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7205423; hg19: chr16-50769262;