Variant 2-60881861-A-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000394479.4(REL):c.10+11A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 1,487,866 control chromosomes in the GnomAD database, including 5,174 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.091 ( 702 hom., cov: 32)

Exomes 𝑓: 0.076 ( 4472 hom. )

Consequence

REL
ENST00000394479.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0670

Variant links:

Genes affected

REL (HGNC:9954): (REL proto-oncogene, NF-kB subunit) This gene encodes a protein that belongs to the Rel homology domain/immunoglobulin-like fold, plexin, transcription factor (RHD/IPT) family. Members of this family regulate genes involved in apoptosis, inflammation, the immune response, and oncogenic processes. This proto-oncogene plays a role in the survival and proliferation of B lymphocytes. Mutation or amplification of this gene is associated with B-cell lymphomas, including Hodgkin's lymphoma. Single nucleotide polymorphisms in this gene are associated with susceptibility to ulcerative colitis and rheumatoid arthritis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2014]

REL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 2-60881861-A-T is Benign according to our data. Variant chr2-60881861-A-T is described in ClinVar as [Benign]. Clinvar id is 1970920.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
REL	NM_001291746.2 linkuse as main transcript	c.10+11A>T	intron_variant	ENST00000394479.4	NP_001278675.1
REL	NM_002908.4 linkuse as main transcript	c.10+11A>T	intron_variant		NP_002899.1
REL	XM_017004627.3 linkuse as main transcript	c.10+11A>T	intron_variant		XP_016860116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
REL	ENST00000394479.4 linkuse as main transcript	c.10+11A>T		intron_variant		1	NM_001291746.2	ENSP00000377989	P1	Q04864-2

Frequencies

GnomAD3 genomes

AF:

0.0908

AC:

13808

AN:

152024

Hom.:

701

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.00440

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.120

Gnomad FIN

AF:

0.0683

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.0708

Gnomad OTH

AF:

0.102

GnomAD3 exomes

AF:

0.107

AC:

9912

AN:

92414

Hom.:

589

AF XY:

0.111

AC XY:

5633

AN XY:

50600

show subpopulations

Gnomad AFR exome

AF:

0.134

Gnomad AMR exome

AF:

0.115

Gnomad ASJ exome

AF:

0.141

Gnomad EAS exome

AF:

0.112

Gnomad SAS exome

AF:

0.145

Gnomad FIN exome

AF:

0.0706

Gnomad NFE exome

AF:

0.0808

Gnomad OTH exome

AF:

0.120

GnomAD4 exome

AF:

0.0760

AC:

101558

AN:

1335724

Hom.:

4472

Cov.:

AF XY:

0.0784

AC XY:

51619

AN XY:

658328

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.108

Gnomad4 ASJ exome

AF:

0.139

Gnomad4 EAS exome

AF:

0.137

Gnomad4 SAS exome

AF:

0.136

Gnomad4 FIN exome

AF:

0.0696

Gnomad4 NFE exome

AF:

0.0658

Gnomad4 OTH exome

AF:

0.0883

GnomAD4 genome

AF:

0.0908

AC:

13815

AN:

152142

Hom.:

702

Cov.:

AF XY:

0.0936

AC XY:

6962

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.115

Gnomad4 AMR

AF:

0.105

Gnomad4 ASJ

AF:

0.148

Gnomad4 EAS

AF:

0.106

Gnomad4 SAS

AF:

0.119

Gnomad4 FIN

AF:

0.0683

Gnomad4 NFE

AF:

0.0708

Gnomad4 OTH

AF:

0.101

Alfa

AF:

0.0515

Hom.:

Bravo

AF:

0.0955

Asia WGS

AF:

0.0980

AC:

342

AN:

3478

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

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.8

DANN

Benign

0.65

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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