rs2237353

chr7-28758597-C-Achr7-28758597-C-Gchr7-28758597-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182898.4(CREB5):c.702+34265C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,048 control chromosomes in the GnomAD database, including 34,400 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 (34400 hom., cov: 32)
• Consequence: CREB5 NM_182898.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CREB5	NM_182898.4	c.702+34265C>A		intron_variant		ENST00000357727.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CREB5	ENST00000357727.7	c.702+34265C>A		intron_variant		1	NM_182898.4	A1

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101007 AN: 151930 Hom.: 34356 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.665 AC: 101109 AN: 152048 Hom.: 34400 Cov.: 32 AF XY: 0.670 AC XY: 49769 AN XY: 74324

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.663

Alfa AF: 0.714 Hom.: 24066

Bravo AF: 0.656

Asia WGS AF: 0.732 AC: 2550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.6
Dann	Benign	0.76

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: rs2237353; hg19: chr7-28798214;