dbSNP rs3136550: CD27-AS1:n.656+428G>A (chr12-6443118-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000399492.6(CD27-AS1):n.656+428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 150,472 control chromosomes in the GnomAD database, including 6,167 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 0.28 ( 6167 hom., cov: 30)

Consequence

CD27-AS1
ENST00000399492.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.14

Publications

10 publications found

Variant links:

Genes affected

CD27-AS1 (HGNC:43896): (CD27 antisense RNA 1)

CD27-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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD27-AS1	NR_015382.2 link	n.1688+428G>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CD27-AS1	ENST00000399492.6 link	n.656+428G>A	intron_variant	Intron 6 of 6	1
CD27-AS1	ENST00000417058.6 link	n.985+428G>A	intron_variant	Intron 2 of 2	1
CD27-AS1	ENST00000537003.2 link	n.2151+428G>A	intron_variant	Intron 5 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.278

AC:

41835

AN:

150366

Hom.:

6164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.339

Gnomad EAS

AF:

0.339

Gnomad SAS

AF:

0.202

Gnomad FIN

AF:

0.360

Gnomad MID

AF:

0.283

Gnomad NFE

AF:

0.311

Gnomad OTH

AF:

0.294

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

GnomAD4 genome

AF:

0.278

AC:

41855

AN:

150472

Hom.:

6167

Cov.:

AF XY:

0.279

AC XY:

20444

AN XY:

73306

show subpopulations

African (AFR)

AF:

0.179

AC:

7360

AN:

41080

American (AMR)

AF:

0.318

AC:

4826

AN:

15168

Ashkenazi Jewish (ASJ)

AF:

0.339

AC:

1174

AN:

3464

East Asian (EAS)

AF:

0.338

AC:

1725

AN:

5102

South Asian (SAS)

AF:

0.202

AC:

969

AN:

4790

European-Finnish (FIN)

AF:

0.360

AC:

3571

AN:

9912

Middle Eastern (MID)

AF:

0.288

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.311

AC:

21080

AN:

67678

Other (OTH)

AF:

0.294

AC:

613

AN:

2084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

1402

2804

4207

5609

7011

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

424

848

1272

1696

2120

<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:

0.305

Hom.:

27609

Bravo

AF:

0.279

Asia WGS

AF:

0.238

AC:

814

AN:

3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.4

(source)

DANN

Benign

0.34

PhyloP100

1.1

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over