chr15-90234035-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000612800.1(CIB1):​c.-150C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 897,370 control chromosomes in the GnomAD database, including 63,668 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.36 (10238 hom., cov: 33)
  • Exomes 𝑓: 0.37 (53430 hom.)
• Consequence: CIB1 ENST00000612800.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.18
• Publications: 6 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: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 15-90234035-G-A is Benign according to our data. Variant chr15-90234035-G-A is described in ClinVar as Benign. ClinVar VariationId is 2688441.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

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>T		non_coding_transcript_exon	Exon 1 of 7
	CIB1	NR_102428.1		n.104-332C>T		intron	N/A
	GDPGP1	NM_001013657.3	MANE Select	c.-399G>A		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>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 7	ENSP00000479860.1	Q99828-2
	CIB1	ENST00000612800.1	TSL:1	c.-150C>T		5_prime_UTR	Exon 1 of 7	ENSP00000479860.1	Q99828-2
	GDPGP1	ENST00000558017.5	TSL:2	c.-193G>A		5_prime_UTR	Exon 1 of 4	ENSP00000452793.1	Q6ZNW5

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55084 AN: 152018 Hom.: 10242 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.383

GnomAD4 exome AF: 0.370 AC: 275675 AN: 745244 Hom.: 53430 Cov.: 10 AF XY: 0.368 AC XY: 136891 AN XY: 372478

African (AFR) AF: 0.365 AC: 5364 AN: 14686

American (AMR) AF: 0.309 AC: 4413 AN: 14262

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 5414 AN: 14104

East Asian (EAS) AF: 0.115 AC: 3155 AN: 27372

South Asian (SAS) AF: 0.273 AC: 12115 AN: 44344

European-Finnish (FIN) AF: 0.337 AC: 9783 AN: 29052

Middle Eastern (MID) AF: 0.416 AC: 1053 AN: 2534

European-Non Finnish (NFE) AF: 0.393 AC: 221395 AN: 563834

Other (OTH) AF: 0.370 AC: 12983 AN: 35056

GnomAD4 genome AF: 0.362 AC: 55108 AN: 152126 Hom.: 10238 Cov.: 33 AF XY: 0.353 AC XY: 26272 AN XY: 74382

African (AFR) AF: 0.368 AC: 15270 AN: 41514

American (AMR) AF: 0.330 AC: 5051 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3470

East Asian (EAS) AF: 0.122 AC: 630 AN: 5168

South Asian (SAS) AF: 0.258 AC: 1247 AN: 4832

European-Finnish (FIN) AF: 0.350 AC: 3707 AN: 10586

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.390 AC: 26482 AN: 67934

Other (OTH) AF: 0.383 AC: 811 AN: 2116

Alfa AF: 0.375 Hom.: 1659

Bravo AF: 0.364

Asia WGS AF: 0.215 AC: 752 AN: 3472

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.68
PhyloP100		2.2
PromoterAI		-0.014	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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;