rs6481941

Variant summary

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

The NM_183011.2(CREM):​c.168+2722G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,078 control chromosomes in the GnomAD database, including 10,601 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 0.37 ( 10601 hom., cov: 33)

Consequence

CREM
NM_183011.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.649
Variant links:
Genes affected
CREM (HGNC:2352): (cAMP responsive element modulator) This gene encodes a bZIP transcription factor that binds to the cAMP responsive element found in many viral and cellular promoters. It is an important component of cAMP-mediated signal transduction during the spermatogenetic cycle, as well as other complex processes. Alternative promoter and translation initiation site usage allows this gene to exert spatial and temporal specificity to cAMP responsiveness. Multiple alternatively spliced transcript variants encoding several different isoforms have been found for this gene, with some of them functioning as activators and some as repressors of transcription. [provided by RefSeq, Jul 2008]

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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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CREMNM_183011.2 linkuse as main transcriptc.168+2722G>A intron_variant ENST00000685392.1 NP_898829.1 Q03060-31

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CREMENST00000685392.1 linkuse as main transcriptc.168+2722G>A intron_variant NM_183011.2 ENSP00000509489.1 Q03060-31

Frequencies

GnomAD3 genomes
AF:
0.370
AC:
56287
AN:
151960
Hom.:
10566
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.429
Gnomad AMI
AF:
0.258
Gnomad AMR
AF:
0.324
Gnomad ASJ
AF:
0.400
Gnomad EAS
AF:
0.317
Gnomad SAS
AF:
0.350
Gnomad FIN
AF:
0.391
Gnomad MID
AF:
0.329
Gnomad NFE
AF:
0.348
Gnomad OTH
AF:
0.369
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.371
AC:
56389
AN:
152078
Hom.:
10601
Cov.:
33
AF XY:
0.370
AC XY:
27519
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.429
Gnomad4 AMR
AF:
0.325
Gnomad4 ASJ
AF:
0.400
Gnomad4 EAS
AF:
0.317
Gnomad4 SAS
AF:
0.351
Gnomad4 FIN
AF:
0.391
Gnomad4 NFE
AF:
0.348
Gnomad4 OTH
AF:
0.375
Alfa
AF:
0.368
Hom.:
1879
Bravo
AF:
0.368
Asia WGS
AF:
0.371
AC:
1288
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.49
DANN
Benign
0.37

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: rs6481941; hg19: chr10-35440141; API