rs217518

Variant summary

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

The NM_182898.4(CREB5):​c.4-5481T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,108 control chromosomes in the GnomAD database, including 7,917 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 0.30 ( 7917 hom., cov: 33)

Consequence

CREB5
NM_182898.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.66
Variant links:
Genes affected
CREB5 (HGNC:16844): (cAMP responsive element binding protein 5) The product of this gene belongs to the CRE (cAMP response element)-binding protein family. Members of this family contain zinc-finger and bZIP DNA-binding domains. The encoded protein specifically binds to CRE as a homodimer or a heterodimer with c-Jun or CRE-BP1, and functions as a CRE-dependent trans-activator. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CREB5NM_182898.4 linkuse as main transcriptc.4-5481T>A intron_variant ENST00000357727.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CREB5ENST00000357727.7 linkuse as main transcriptc.4-5481T>A intron_variant 1 NM_182898.4 A1Q02930-1

Frequencies

GnomAD3 genomes
AF:
0.303
AC:
46092
AN:
151990
Hom.:
7918
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.147
Gnomad AMI
AF:
0.231
Gnomad AMR
AF:
0.356
Gnomad ASJ
AF:
0.468
Gnomad EAS
AF:
0.150
Gnomad SAS
AF:
0.325
Gnomad FIN
AF:
0.371
Gnomad MID
AF:
0.389
Gnomad NFE
AF:
0.377
Gnomad OTH
AF:
0.344
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.303
AC:
46096
AN:
152108
Hom.:
7917
Cov.:
33
AF XY:
0.303
AC XY:
22518
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.147
Gnomad4 AMR
AF:
0.356
Gnomad4 ASJ
AF:
0.468
Gnomad4 EAS
AF:
0.150
Gnomad4 SAS
AF:
0.325
Gnomad4 FIN
AF:
0.371
Gnomad4 NFE
AF:
0.377
Gnomad4 OTH
AF:
0.342
Alfa
AF:
0.328
Hom.:
1058
Bravo
AF:
0.293
Asia WGS
AF:
0.252
AC:
876
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.58
CADD
Benign
11
DANN
Benign
0.55

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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.

Other links and lift over

dbSNP: rs217518; hg19: chr7-28522312; API