rs10233653

Variant names:

• chr7-28400701-G-A
• rs10233653
• ENST00000396299.6:c.-24-94205G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-28400701-G-A
• chr7-28400701-G-C

Variant summary

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

The NM_182899.5(CREB5):​c.-24-94205G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,028 control chromosomes in the GnomAD database, including 8,056 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 0.31 (8056 hom., cov: 32)
• Consequence: CREB5 NM_182899.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 5 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 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.-24-94205G>A		intron	N/A	NP_878902.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CREB5	ENST00000396299.6	TSL:1	c.-24-94205G>A		intron	N/A	ENSP00000379593.2

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46496 AN: 151910 Hom.: 8051 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.306 AC: 46507 AN: 152028 Hom.: 8056 Cov.: 32 AF XY: 0.308 AC XY: 22892 AN XY: 74296

African (AFR) AF: 0.131 AC: 5443 AN: 41520

American (AMR) AF: 0.369 AC: 5641 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2037 AN: 5160

South Asian (SAS) AF: 0.357 AC: 1717 AN: 4810

European-Finnish (FIN) AF: 0.360 AC: 3801 AN: 10552

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.373 AC: 25361 AN: 67928

Other (OTH) AF: 0.333 AC: 702 AN: 2106

Alfa AF: 0.353 Hom.: 42180

Bravo AF: 0.299

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	14
DANN	Benign	0.73
PhyloP100		1.1
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: rs10233653; hg19: chr7-28440320;