Genetic Variant CD27-AS1:n.656+1091_656+1093delTTT (chr12-6442452-CAAA-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000399492.6(CD27-AS1):n.656+1091_656+1093delTTT 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 0.0012 ( 0 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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD27-AS1	NR_015382.2 link	n.1688+1091_1688+1093delTTT		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CD27-AS1	ENST00000399492.6 link	n.656+1091_656+1093delTTT	intron_variant	Intron 6 of 6	1
CD27-AS1	ENST00000417058.6 link	n.985+1091_985+1093delTTT	intron_variant	Intron 2 of 2	1
CD27-AS1	ENST00000537003.2 link	n.2151+1091_2151+1093delTTT	intron_variant	Intron 5 of 5	1

Frequencies

GnomAD3 genomes

AF:

0.00115

AC:

113

AN:

98414

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00267

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00101

Gnomad ASJ

AF:

0.000747

Gnomad EAS

AF:

0.000292

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00135

Gnomad MID

AF:

0.00476

Gnomad NFE

AF:

0.000504

Gnomad OTH

AF:

0.00225

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

GnomAD4 genome

AF:

0.00119

AC:

117

AN:

98402

Hom.:

Cov.:

AF XY:

0.00109

AC XY:

AN XY:

45948

show subpopulations

African (AFR)

AF:

0.00274

AC:

AN:

25152

American (AMR)

AF:

0.00101

AC:

AN:

8902

Ashkenazi Jewish (ASJ)

AF:

0.000747

AC:

AN:

2678

East Asian (EAS)

AF:

0.000293

AC:

AN:

3418

South Asian (SAS)

AF:

0.00

AC:

AN:

2736

European-Finnish (FIN)

AF:

0.00135

AC:

AN:

3704

Middle Eastern (MID)

AF:

0.00521

AC:

AN:

192

European-Non Finnish (NFE)

AF:

0.000504

AC:

AN:

49566

Other (OTH)

AF:

0.00373

AC:

AN:

1342

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

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-CAAAAAAAAA

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