dbSNP rs8056611: CYLD-AS1:n.871-1376T>C (chr16-50733736-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000563315.2(CYLD-AS1):n.871-1376T>C variant causes a intron 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
ENST00000563315.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0770

Publications

14 publications found

Variant links:

Genes affected

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

CYLD-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CYLD-AS1	NR_184278.1 link	n.803-1376T>C		intron_variant	Intron 2 of 5
CYLD-AS1	NR_184279.1 link	n.270-1376T>C		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYLD-AS1	ENST00000563315.2 link	n.871-1376T>C		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.552

AC:

83857

AN:

151788

Hom.:

24029

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.550

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.550

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.553

AC:

83967

AN:

151904

Hom.:

24082

Cov.:

AF XY:

0.549

AC XY:

40776

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.704

AC:

29147

AN:

41388

American (AMR)

AF:

0.479

AC:

7309

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.671

AC:

2328

AN:

3472

East Asian (EAS)

AF:

0.253

AC:

1303

AN:

5156

South Asian (SAS)

AF:

0.466

AC:

2239

AN:

4806

European-Finnish (FIN)

AF:

0.515

AC:

5439

AN:

10552

Middle Eastern (MID)

AF:

0.520

AC:

153

AN:

294

European-Non Finnish (NFE)

AF:

0.507

AC:

34437

AN:

67952

Other (OTH)

AF:

0.518

AC:

1089

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1785

3570

5354

7139

8924

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

708

1416

2124

2832

3540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.526

Hom.:

6477

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

(source)

DANN

Benign

0.24

PhyloP100

0.077

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over