chr7-137896069-T-C

Variant names:

• chr7-137896069-T-C
• rs273940
• NM_194071.4:c.1043+5285A>G

Variant summary

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

The NM_194071.4(CREB3L2):​c.1043+5285A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,160 control chromosomes in the GnomAD database, including 38,220 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 0.71 (38220 hom., cov: 33)
• Consequence: CREB3L2 NM_194071.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 4 publications found

Genes affected

CREB3L2 (HGNC:23720): (cAMP responsive element binding protein 3 like 2) This gene encodes a member of the oasis bZIP transcription factor family. Members of this family can dimerize but form homodimers only. The encoded protein is a transcriptional activator. Translocations between this gene on chromosome 7 and the gene fused in sarcoma on chromosome 16 can be found in some tumors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CREB3L2	NM_194071.4	c.1043+5285A>G		intron_variant	Intron 8 of 11	ENST00000330387.11	NP_919047.2
CREB3L2	NM_001318246.2	c.854+5285A>G		intron_variant	Intron 8 of 11		NP_001305175.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CREB3L2	ENST00000330387.11	c.1043+5285A>G		intron_variant	Intron 8 of 11	1	NM_194071.4	ENSP00000329140.6
CREB3L2	ENST00000456390.5	c.1043+5285A>G		intron_variant	Intron 8 of 9	2		ENSP00000403550.1

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107588 AN: 152042 Hom.: 38175 Cov.: 33

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.708 AC: 107689 AN: 152160 Hom.: 38220 Cov.: 33 AF XY: 0.710 AC XY: 52811 AN XY: 74390

African (AFR) AF: 0.715 AC: 29661 AN: 41506

American (AMR) AF: 0.757 AC: 11575 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2382 AN: 3470

East Asian (EAS) AF: 0.754 AC: 3898 AN: 5168

South Asian (SAS) AF: 0.660 AC: 3182 AN: 4820

European-Finnish (FIN) AF: 0.718 AC: 7605 AN: 10594

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47019 AN: 67990

Other (OTH) AF: 0.729 AC: 1539 AN: 2112

Alfa AF: 0.688 Hom.: 4496

Bravo AF: 0.717

Asia WGS AF: 0.707 AC: 2459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.029
DANN	Benign	0.46
PhyloP100		-1.7
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: rs273940; hg19: chr7-137580815;