11-65663889-C-T

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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0600
Variant links:
Genes affected
RELA-DT (HGNC:54185): (RELA divergent transcript)
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]

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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-DTNR_183625.1 linkn.143+741C>T intron_variant
RELANM_001404662.1 linkc.-806G>A upstream_gene_variant NP_001391591.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RELA-DTENST00000654031.1 linkn.605C>T non_coding_transcript_exon_variant 2/4
RELA-DTENST00000685480.2 linkn.822C>T non_coding_transcript_exon_variant 1/1
RELA-DTENST00000648185.2 linkn.403+206C>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.168
AC:
25587
AN:
152062
Hom.:
2666
Cov.:
31
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.:
31
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.

Other links and lift over

dbSNP: rs7101916; hg19: chr11-65431360; API