Genetic Variant CD27-AS1:n.656+1092_656+1093delTT (chr12-6442452-CAA-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000399492.6(CD27-AS1):n.656+1092_656+1093delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 813 hom., cov: 0)

Consequence

CD27-AS1
ENST00000399492.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.29

Publications

1 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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 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+1092_1688+1093delTT		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CD27-AS1	ENST00000399492.6 link	n.656+1092_656+1093delTT	intron_variant	Intron 6 of 6	1
CD27-AS1	ENST00000417058.6 link	n.985+1092_985+1093delTT	intron_variant	Intron 2 of 2	1
CD27-AS1	ENST00000537003.2 link	n.2151+1092_2151+1093delTT	intron_variant	Intron 5 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

15685

AN:

98470

Hom.:

811

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.197

Gnomad AMR

AF:

0.154

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.199

Gnomad MID

AF:

0.163

Gnomad NFE

AF:

0.174

Gnomad OTH

AF:

0.156

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

GnomAD4 genome

AF:

0.159

AC:

15688

AN:

98454

Hom.:

813

Cov.:

AF XY:

0.157

AC XY:

7205

AN XY:

45972

show subpopulations

African (AFR)

AF:

0.133

AC:

3342

AN:

25178

American (AMR)

AF:

0.153

AC:

1369

AN:

8920

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

485

AN:

2682

East Asian (EAS)

AF:

0.134

AC:

457

AN:

3420

South Asian (SAS)

AF:

0.112

AC:

306

AN:

2734

European-Finnish (FIN)

AF:

0.199

AC:

740

AN:

3712

Middle Eastern (MID)

AF:

0.158

AC:

AN:

190

European-Non Finnish (NFE)

AF:

0.174

AC:

8608

AN:

49560

Other (OTH)

AF:

0.156

AC:

210

AN:

1344

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

583

1165

1748

2330

2913

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.3

Splicing

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

Publications

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12-6442452-CAAAAAAAAAAAA-CAAAAAAAAAA

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