Variant chr12-6444640-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NR_015382.2(CD27-AS1):n.1517-923C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.27 ( 3948 hom., cov: 19)

Consequence

CD27-AS1
NR_015382.2 intron, non_coding_transcript

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.45

Variant links:

Genes affected

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

CD27-AS1 links:

CD27 (HGNC:):

CD27 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 12-6444640-G-A is Benign according to our data. Variant chr12-6444640-G-A is described in ClinVar as [Benign]. Clinvar id is 1228878.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
CD27-AS1	NR_015382.2 linkuse as main transcript	n.1517-923C>T	intron_variant, non_coding_transcript_variant
CD27	NM_001413266.1 linkuse as main transcript	c.-315+521G>A	intron_variant	NP_001400195.1
CD27	NM_001413267.1 linkuse as main transcript	c.-403+521G>A	intron_variant	NP_001400196.1
CD27	NM_001413268.1 linkuse as main transcript	c.-315+33G>A	intron_variant	NP_001400197.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD27-AS1	ENST00000689782.1 linkuse as main transcript	n.460-923C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

32265

AN:

121388

Hom.:

3943

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.429

Gnomad AMR

AF:

0.367

Gnomad ASJ

AF:

0.290

Gnomad EAS

AF:

0.362

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.328

Gnomad MID

AF:

0.356

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.299

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

GnomAD4 genome

AF:

0.266

AC:

32286

AN:

121458

Hom.:

3948

Cov.:

AF XY:

0.272

AC XY:

15386

AN XY:

56652

show subpopulations

Gnomad4 AFR

AF:

0.196

Gnomad4 AMR

AF:

0.368

Gnomad4 ASJ

AF:

0.290

Gnomad4 EAS

AF:

0.362

Gnomad4 SAS

AF:

0.229

Gnomad4 FIN

AF:

0.328

Gnomad4 NFE

AF:

0.269

Gnomad4 OTH

AF:

0.299

Alfa

AF:

0.260

Hom.:

7167

Bravo

AF:

0.245

Asia WGS

AF:

0.234

AC:

808

AN:

3468

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

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.5

DANN

Benign

0.48

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over