rs11765845

Variant names:

• chr7-28351523-A-G
• rs11765845
• ENST00000396299.6:c.-25+52082A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-28351523-A-G
• chr7-28351523-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_182899.5(CREB5):​c.-25+52082A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,046 control chromosomes in the GnomAD database, including 34,183 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 0.66 (34183 hom., cov: 32)
• Consequence: CREB5 NM_182899.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 15 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182899.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CREB5	NM_182899.5		c.-25+52082A>G		intron	N/A	NP_878902.2	Q02930-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CREB5	ENST00000396299.6	TSL:1	c.-25+52082A>G		intron	N/A	ENSP00000379593.2	Q02930-3

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100646 AN: 151928 Hom.: 34165 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.662 AC: 100706 AN: 152046 Hom.: 34183 Cov.: 32 AF XY: 0.661 AC XY: 49112 AN XY: 74314

African (AFR) AF: 0.509 AC: 21094 AN: 41420

American (AMR) AF: 0.721 AC: 11023 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2318 AN: 3468

East Asian (EAS) AF: 0.706 AC: 3660 AN: 5186

South Asian (SAS) AF: 0.766 AC: 3691 AN: 4818

European-Finnish (FIN) AF: 0.667 AC: 7044 AN: 10564

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49394 AN: 67982

Other (OTH) AF: 0.691 AC: 1461 AN: 2114

Alfa AF: 0.705 Hom.: 146927

Bravo AF: 0.659

Asia WGS AF: 0.701 AC: 2439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	11
DANN	Benign	0.70
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11765845; hg19: chr7-28391142;