rs11569360

Variant names:

• chr12-6444626-C-A
• rs11569360
• ENST00000399492.6:n.485-909G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-6444626-C-A
• chr12-6444626-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001413266.1(CD27):​c.-315+507C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.021 (98 hom., cov: 20)
• Consequence: CD27 NM_001413266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 1 publications found

Genes affected

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

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 Gene-Disease associations (from GenCC):

• lymphoproliferative syndrome 2

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• autosomal recessive lymphoproliferative disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD27	NM_001413266.1	c.-315+507C>A		intron_variant	Intron 1 of 5		NP_001400195.1
CD27	NM_001413267.1	c.-403+507C>A		intron_variant	Intron 1 of 6		NP_001400196.1
CD27	NM_001413268.1	c.-315+19C>A		intron_variant	Intron 1 of 5		NP_001400197.1
CD27-AS1	NR_015382.2	n.1517-909G>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD27-AS1	ENST00000399492.6	n.485-909G>T		intron_variant	Intron 5 of 6	1
CD27-AS1	ENST00000417058.6	n.814-909G>T		intron_variant	Intron 1 of 2	1
CD27-AS1	ENST00000537003.2	n.1980-909G>T		intron_variant	Intron 4 of 5	1

Frequencies

GnomAD3 genomes AF: 0.0211 AC: 2766 AN: 131298 Hom.: 95 Cov.: 20

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.00118

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0135

Gnomad NFE AF: 0.000510

Gnomad OTH AF: 0.0158

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

GnomAD4 genome AF: 0.0212 AC: 2780 AN: 131340 Hom.: 98 Cov.: 20 AF XY: 0.0207 AC XY: 1278 AN XY: 61854

African (AFR) AF: 0.0763 AC: 2581 AN: 33812

American (AMR) AF: 0.0118 AC: 132 AN: 11180

Ashkenazi Jewish (ASJ) AF: 0.00118 AC: 4 AN: 3380

East Asian (EAS) AF: 0.00 AC: 0 AN: 4408

South Asian (SAS) AF: 0.00 AC: 0 AN: 4126

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6952

Middle Eastern (MID) AF: 0.0142 AC: 3 AN: 212

European-Non Finnish (NFE) AF: 0.000510 AC: 33 AN: 64684

Other (OTH) AF: 0.0157 AC: 27 AN: 1720

Alfa AF: 0.00 Hom.: 122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.074
DANN	Benign	0.21
PhyloP100		-1.7
PromoterAI		0.037	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11569360; hg19: chr12-6553792;