Variant 12-6442452-CAAAAAAAAAAAA-CAAAAAAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000399492.6(CD27-AS1):n.656+1090_656+1093delTTTT 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 0.0024 ( 1 hom., cov: 0)

Consequence

CD27-AS1
ENST00000399492.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.29

Variant links:

Genes affected

CD27-AS1 (HGNC:):

CD27-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD27-AS1	NR_015382.2 linkuse as main transcript	n.1688+1090_1688+1093delTTTT		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CD27-AS1	ENST00000399492.6 linkuse as main transcript	n.656+1090_656+1093delTTTT	intron_variant	1
CD27-AS1	ENST00000417058.6 linkuse as main transcript	n.985+1090_985+1093delTTTT	intron_variant	1
CD27-AS1	ENST00000537003.2 linkuse as main transcript	n.2151+1090_2151+1093delTTTT	intron_variant	1

Frequencies

GnomAD3 genomes

AF:

0.00245

AC:

241

AN:

98426

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00820

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00292

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000270

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000101

Gnomad OTH

AF:

0.00225

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

GnomAD4 genome

AF:

0.00245

AC:

241

AN:

98414

Hom.:

Cov.:

AF XY:

0.00246

AC XY:

113

AN XY:

45956

show subpopulations

Gnomad4 AFR

AF:

0.00819

Gnomad4 AMR

AF:

0.00292

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000270

Gnomad4 NFE

AF:

0.000101

Gnomad4 OTH

AF:

0.00224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over