Genetic Variant ENST00000399492.6: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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000399492.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399492.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD27-AS1	NR_015382.2		n.1688+1091_1688+1093delTTT		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
CD27-AS1	ENST00000399492.6	TSL:1	n.656+1091_656+1093delTTT	intron	N/A
CD27-AS1	ENST00000417058.6	TSL:1	n.985+1091_985+1093delTTT	intron	N/A
CD27-AS1	ENST00000537003.2	TSL:1	n.2151+1091_2151+1093delTTT	intron	N/A

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 v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over