Variant 12-6444664-TG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001413266.1(CD27):c.-315+554delG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 1676 hom., cov: 0)

Consequence

CD27
NM_001413266.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.06

Variant links:

Genes affected

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

CD27-AS1 links:

CD27 (HGNC:11922): (CD27 molecule) The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor is required for generation and long-term maintenance of T cell immunity. It binds to ligand CD70, and plays a key role in regulating B-cell activation and immunoglobulin synthesis. This receptor transduces signals that lead to the activation of NF-kappaB and MAPK8/JNK. Adaptor proteins TRAF2 and TRAF5 have been shown to mediate the signaling process of this receptor. CD27-binding protein (SIVA), a proapoptotic protein, can bind to this receptor and is thought to play an important role in the apoptosis induced by this receptor. [provided by RefSeq, Jul 2008]

CD27 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 12-6444664-TG-T is Benign according to our data. Variant chr12-6444664-TG-T is described in ClinVar as [Benign]. Clinvar id is 1256950.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
CD27	NM_001413266.1 link	c.-315+554delG	intron_variant	NP_001400195.1
CD27	NM_001413267.1 link	c.-403+554delG	intron_variant	NP_001400196.1
CD27	NM_001413268.1 link	c.-315+66delG	intron_variant	NP_001400197.1
CD27-AS1	NR_015382.2 link	n.1517-948delC	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CD27-AS1	ENST00000399492.6 link	n.485-948delC	intron_variant	1
CD27-AS1	ENST00000417058.6 link	n.814-948delC	intron_variant	1
CD27-AS1	ENST00000537003.2 link	n.1980-948delC	intron_variant	1

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

19760

AN:

70918

Hom.:

1679

Cov.:

show subpopulations

Gnomad AFR

AF:

0.259

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.215

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.132

Gnomad SAS

AF:

0.398

Gnomad FIN

AF:

0.251

Gnomad MID

AF:

0.260

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.253

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

GnomAD4 genome

AF:

0.278

AC:

19748

AN:

70932

Hom.:

1676

Cov.:

AF XY:

0.277

AC XY:

8970

AN XY:

32380

show subpopulations

Gnomad4 AFR

AF:

0.259

Gnomad4 AMR

AF:

0.214

Gnomad4 ASJ

AF:

0.208

Gnomad4 EAS

AF:

0.132

Gnomad4 SAS

AF:

0.395

Gnomad4 FIN

AF:

0.251

Gnomad4 NFE

AF:

0.305

Gnomad4 OTH

AF:

0.252

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

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.