chr15-90571144-A-T

Variant names:

• chr15-90571144-A-T
• rs12915189
• NM_022769.5:c.232-22492A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_022769.5(CRTC3):​c.232-22492A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: CRTC3 NM_022769.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 19 publications found

Genes affected

CRTC3 (HGNC:26148): (CREB regulated transcription coactivator 3) This gene is a member of the CREB regulated transcription coactivator gene family. This family regulates CREB-dependent gene transcription in a phosphorylation-independent manner and may be selective for cAMP-responsive genes. The protein encoded by this gene may induce mitochondrial biogenesis and attenuate catecholamine signaling in adipose tissue. A translocation event between this gene and Notch coactivator mastermind-like gene 2, which results in a fusion protein, has been reported in mucoepidermoid carcinomas. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRTC3	NM_022769.5	c.232-22492A>T		intron_variant	Intron 2 of 14	ENST00000268184.11	NP_073606.3
CRTC3	NM_001042574.3	c.232-22492A>T		intron_variant	Intron 2 of 14		NP_001036039.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRTC3	ENST00000268184.11	c.232-22492A>T		intron_variant	Intron 2 of 14	1	NM_022769.5	ENSP00000268184.6
CRTC3	ENST00000420329.6	c.232-22492A>T		intron_variant	Intron 2 of 14	2		ENSP00000416573.2
CRTC3	ENST00000686240.1	n.232-22492A>T		intron_variant	Intron 2 of 13			ENSP00000508866.1
CRTC3	ENST00000687075.1	n.55-22492A>T		intron_variant	Intron 1 of 8			ENSP00000510590.1
CRTC3	ENST00000691029.1	n.232-22492A>T		intron_variant	Intron 2 of 16			ENSP00000510507.1
CRTC3	ENST00000692149.1	n.232-22492A>T		intron_variant	Intron 2 of 12			ENSP00000510448.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.024
DANN	Benign	0.71
PhyloP100		-1.8

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: rs12915189; hg19: chr15-91114376;