Variant 11-65663889-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000654031.1(RELA-DT):n.605C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,180 control chromosomes in the GnomAD database, including 2,672 homozygotes. 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 0.17 ( 2672 hom., cov: 31)

Consequence

RELA-DT
ENST00000654031.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0600

Variant links:

Genes affected

RELA-DT (HGNC:54185): (RELA divergent transcript)

RELA-DT links:

RELA (HGNC:9955): (RELA proto-oncogene, NF-kB subunit) NF-kappa-B is a ubiquitous transcription factor involved in several biological processes. It is held in the cytoplasm in an inactive state by specific inhibitors. Upon degradation of the inhibitor, NF-kappa-B moves to the nucleus and activates transcription of specific genes. NF-kappa-B is composed of NFKB1 or NFKB2 bound to either REL, RELA, or RELB. The most abundant form of NF-kappa-B is NFKB1 complexed with the product of this gene, RELA. Four transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

RELA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RELA-DT	NR_183625.1 link	n.143+741C>T		intron_variant
RELA	NM_001404662.1 link	c.-806G>A		upstream_gene_variant			NP_001391591.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons
RELA-DT	ENST00000654031.1 link	n.605C>T	non_coding_transcript_exon_variant	2/4
RELA-DT	ENST00000685480.2 link	n.822C>T	non_coding_transcript_exon_variant	1/1
RELA-DT	ENST00000648185.2 link	n.403+206C>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25587

AN:

152062

Hom.:

2666

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.0943

Gnomad AMR

AF:

0.295

Gnomad ASJ

AF:

0.123

Gnomad EAS

AF:

0.381

Gnomad SAS

AF:

0.0937

Gnomad FIN

AF:

0.0898

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.163

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

GnomAD4 genome

AF:

0.168

AC:

25610

AN:

152180

Hom.:

2672

Cov.:

AF XY:

0.169

AC XY:

12599

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.207

Gnomad4 AMR

AF:

0.295

Gnomad4 ASJ

AF:

0.123

Gnomad4 EAS

AF:

0.381

Gnomad4 SAS

AF:

0.0942

Gnomad4 FIN

AF:

0.0898

Gnomad4 NFE

AF:

0.121

Gnomad4 OTH

AF:

0.160

Alfa

AF:

0.137

Hom.:

2462

Bravo

AF:

0.194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

5.4

DANN

Benign

0.68

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