2-207573836-A-G

Variant names:

• chr2-207573836-A-G
• rs2551922
• NM_004379.5:c.506-1436A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004379.5(CREB1):​c.506-1436A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,256 control chromosomes in the GnomAD database, including 60,410 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 0.88 (60410 hom., cov: 33)
• Consequence: CREB1 NM_004379.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 7 publications found

Genes affected

CREB1 (HGNC:2345): (cAMP responsive element binding protein 1) This gene encodes a transcription factor that is a member of the leucine zipper family of DNA binding proteins. This protein binds as a homodimer to the cAMP-responsive element, an octameric palindrome. The protein is phosphorylated by several protein kinases, and induces transcription of genes in response to hormonal stimulation of the cAMP pathway. Alternate splicing of this gene results in several transcript variants encoding different isoforms. [provided by RefSeq, Mar 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004379.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CREB1	NM_004379.5	MANE Select	c.506-1436A>G		intron	N/A	NP_004370.1
	CREB1	NM_001371426.1		c.548-1436A>G		intron	N/A	NP_001358355.1
	CREB1	NM_134442.5		c.548-1436A>G		intron	N/A	NP_604391.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CREB1	ENST00000353267.8	TSL:1 MANE Select	c.506-1436A>G		intron	N/A	ENSP00000236995.3
	CREB1	ENST00000432329.6	TSL:1	c.548-1436A>G		intron	N/A	ENSP00000387699.2
	CREB1	ENST00000430624.5	TSL:5	c.506-1436A>G		intron	N/A	ENSP00000405539.1

Frequencies

GnomAD3 genomes AF: 0.881 AC: 134025 AN: 152138 Hom.: 60375 Cov.: 33

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.881 AC: 134118 AN: 152256 Hom.: 60410 Cov.: 33 AF XY: 0.883 AC XY: 65777 AN XY: 74458

African (AFR) AF: 0.670 AC: 27791 AN: 41490

American (AMR) AF: 0.930 AC: 14230 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3140 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5179 AN: 5182

South Asian (SAS) AF: 0.984 AC: 4753 AN: 4830

European-Finnish (FIN) AF: 0.974 AC: 10339 AN: 10616

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.967 AC: 65792 AN: 68042

Other (OTH) AF: 0.888 AC: 1878 AN: 2116

Alfa AF: 0.907 Hom.: 9253

Bravo AF: 0.869

Asia WGS AF: 0.969 AC: 3372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.49
PhyloP100		-0.30
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2551922; hg19: chr2-208438560;