chr7-28562146-G-A

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CREB5	NM_182898.4	c.292-8219G>A		intron_variant	Intron 4 of 10	ENST00000357727.7	NP_878901.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CREB5	ENST00000357727.7	c.292-8219G>A		intron_variant	Intron 4 of 10	1	NM_182898.4	ENSP00000350359.2

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

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.901

Alfa AF: 0.863 Hom.: 21495

Bravo AF: 0.888

Asia WGS AF: 0.942 AC: 3278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.62

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

Publications

LitVar

Other links and lift over

dbSNP: rs216744; hg19: chr7-28601764;