15-90234035-G-C

Variant names:

• chr15-90234035-G-C
• rs8025979
• ENST00000612800.1:c.-150C>G

Variant summary

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

The ENST00000612800.1(CIB1):​c.-150C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000134 in 746,724 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: 33)
  • Exomes 𝑓: 0.0000013 (0 hom.)
• Consequence: CIB1 ENST00000612800.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18
• Publications: 0 publications found

Genes affected

CIB1 (HGNC:16920): (calcium and integrin binding 1) This gene encodes a member of the EF-hand domain-containing calcium-binding superfamily. The encoded protein interacts with many other proteins, including the platelet integrin alpha-IIb-beta-3, DNA-dependent protein kinase, presenilin-2, focal adhesion kinase, p21 activated kinase, and protein kinase D. The encoded protein may be involved in cell survival and proliferation, and is associated with several disease states including cancer and Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]

GDPGP1 (HGNC:34360): (GDP-D-glucose phosphorylase 1) Enables GDP-D-glucose phosphorylase activity. Involved in glucose metabolic process. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000284626 (HGNC:):

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=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612800.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIB1	NR_102427.1		n.121C>G		non_coding_transcript_exon	Exon 1 of 7
	CIB1	NR_102428.1		n.104-332C>G		intron	N/A
	GDPGP1	NM_001013657.3	MANE Select	c.-399G>C		upstream_gene	N/A	NP_001013679.2	Q6ZNW5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIB1	ENST00000612800.1	TSL:1	c.-150C>G		5_prime_UTR	Exon 1 of 7	ENSP00000479860.1	Q99828-2
	GDPGP1	ENST00000558017.5	TSL:2	c.-193G>C		5_prime_UTR	Exon 1 of 4	ENSP00000452793.1	Q6ZNW5
	GDPGP1	ENST00000899066.1		c.-628G>C		5_prime_UTR	Exon 1 of 3	ENSP00000569125.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000134 AC: 1 AN: 746724 Hom.: 0 Cov.: 10 AF XY: 0.00000268 AC XY: 1 AN XY: 373138

African (AFR) AF: 0.00 AC: 0 AN: 14706

American (AMR) AF: 0.00 AC: 0 AN: 14280

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14122

East Asian (EAS) AF: 0.00 AC: 0 AN: 27382

South Asian (SAS) AF: 0.00 AC: 0 AN: 44416

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29072

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2536

European-Non Finnish (NFE) AF: 0.00000177 AC: 1 AN: 565088

Other (OTH) AF: 0.00 AC: 0 AN: 35122

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	11
DANN	Benign	0.52
PhyloP100		2.2
PromoterAI		-0.21	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs8025979; hg19: chr15-90777267;