chr15-90617932-G-C

Variant names:

• chr15-90617932-G-C
• rs77748519
• NM_022769.5:c.663G>C

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_022769.5(CRTC3):​c.663G>C​(p.Pro221Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,828 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 31)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: CRTC3 NM_022769.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

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

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP7: Synonymous conserved (PhyloP=-0.209 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRTC3	NM_022769.5	c.663G>C	p.Pro221Pro	synonymous_variant	Exon 8 of 15	ENST00000268184.11	NP_073606.3
CRTC3	NM_001042574.3	c.663G>C	p.Pro221Pro	synonymous_variant	Exon 8 of 15		NP_001036039.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRTC3	ENST00000268184.11	c.663G>C	p.Pro221Pro	synonymous_variant	Exon 8 of 15	1	NM_022769.5	ENSP00000268184.6
CRTC3	ENST00000420329.6	c.663G>C	p.Pro221Pro	synonymous_variant	Exon 8 of 15	2		ENSP00000416573.2
CRTC3	ENST00000558005.1	c.318G>C	p.Pro106Pro	synonymous_variant	Exon 5 of 7	4		ENSP00000452676.1
CRTC3	ENST00000686240.1	n.*76G>C		non_coding_transcript_exon_variant	Exon 7 of 14			ENSP00000508866.1
CRTC3	ENST00000687075.1	n.486G>C		non_coding_transcript_exon_variant	Exon 7 of 9			ENSP00000510590.1
CRTC3	ENST00000691029.1	n.663G>C		non_coding_transcript_exon_variant	Exon 8 of 17			ENSP00000510507.1
CRTC3	ENST00000686240.1	n.*76G>C		3_prime_UTR_variant	Exon 7 of 14			ENSP00000508866.1
CRTC3	ENST00000692149.1	n.*27-1809G>C		intron_variant	Intron 6 of 12			ENSP00000510448.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.85e-7 AC: 1 AN: 1460828 Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1 AN XY: 726814

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	6.7
DANN	Benign	0.74
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs77748519; hg19: chr15-91161164;