NM_182898.4:c.292-8219G>A

Variant names:

• chr7-28562146-G-A
• rs216744
• NM_182898.4:c.292-8219G>A

Variant summary

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

The NM_182898.4(CREB5):​c.292-8219G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 152,314 control chromosomes in the GnomAD database, including 59,712 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 (59712 hom., cov: 33)
• Consequence: CREB5 NM_182898.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.589
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182898.4. 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
	CREB5	NM_182898.4	MANE Select	c.292-8219G>A		intron	N/A	NP_878901.2
	CREB5	NM_004904.4		c.271-8219G>A		intron	N/A	NP_004895.2
	CREB5	NM_182899.5		c.193-8219G>A		intron	N/A	NP_878902.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CREB5	ENST00000357727.7	TSL:1 MANE Select	c.292-8219G>A		intron	N/A	ENSP00000350359.2
	CREB5	ENST00000396300.6	TSL:1	c.271-8219G>A		intron	N/A	ENSP00000379594.2
	CREB5	ENST00000396299.6	TSL:1	c.193-8219G>A		intron	N/A	ENSP00000379593.2

Frequencies

GnomAD3 genomes AF: 0.885 AC: 134689 AN: 152196 Hom.: 59677 Cov.: 33

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.963

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.885 AC: 134776 AN: 152314 Hom.: 59712 Cov.: 33 AF XY: 0.888 AC XY: 66122 AN XY: 74468

African (AFR) AF: 0.914 AC: 38013 AN: 41572

American (AMR) AF: 0.899 AC: 13764 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3229 AN: 3472

East Asian (EAS) AF: 0.943 AC: 4886 AN: 5184

South Asian (SAS) AF: 0.962 AC: 4647 AN: 4830

European-Finnish (FIN) AF: 0.868 AC: 9203 AN: 10608

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58049 AN: 68026

Other (OTH) AF: 0.901 AC: 1904 AN: 2114

Alfa AF: 0.864 Hom.: 24699

Bravo AF: 0.888

Asia WGS AF: 0.942 AC: 3278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		0.59
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: rs216744; hg19: chr7-28601764;