rs10932201

Variant names:

• chr2-207561533-G-A
• rs10932201
• NM_004379.5:c.261+1161G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-207561533-G-A
• chr2-207561533-G-C

Variant summary

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

The NM_004379.5(CREB1):​c.261+1161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,910 control chromosomes in the GnomAD database, including 12,886 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 0.39 (12886 hom., cov: 31)
• Consequence: CREB1 NM_004379.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 23 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=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CREB1	NM_004379.5	c.261+1161G>A		intron_variant	Intron 3 of 7	ENST00000353267.8	NP_004370.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CREB1	ENST00000353267.8	c.261+1161G>A		intron_variant	Intron 3 of 7	1	NM_004379.5	ENSP00000236995.3

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58903 AN: 151794 Hom.: 12881 Cov.: 31

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.388 AC: 58915 AN: 151910 Hom.: 12886 Cov.: 31 AF XY: 0.393 AC XY: 29199 AN XY: 74234

African (AFR) AF: 0.179 AC: 7429 AN: 41424

American (AMR) AF: 0.446 AC: 6802 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3468

East Asian (EAS) AF: 0.638 AC: 3305 AN: 5180

South Asian (SAS) AF: 0.429 AC: 2063 AN: 4814

European-Finnish (FIN) AF: 0.485 AC: 5107 AN: 10526

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31076 AN: 67930

Other (OTH) AF: 0.436 AC: 919 AN: 2108

Alfa AF: 0.438 Hom.: 19334

Bravo AF: 0.375

Asia WGS AF: 0.501 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	8.3
DANN	Benign	0.87
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10932201; hg19: chr2-208426257;