rs2497

Variant names:

• chr10-5765645-A-G
• rs2497
• NM_001494.4:c.*361T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-5765645-A-G
• chr10-5765645-A-T

Variant summary

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

The NM_001494.4(GDI2):​c.*361T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 168,756 control chromosomes in the GnomAD database, including 10,595 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 0.35 (9392 hom., cov: 31)
  • Exomes 𝑓: 0.36 (1203 hom.)
• Consequence: GDI2 NM_001494.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 8 publications found

Genes affected

GDI2 (HGNC:4227): (GDP dissociation inhibitor 2) GDP dissociation inhibitors are proteins that regulate the GDP-GTP exchange reaction of members of the rab family, small GTP-binding proteins of the ras superfamily, that are involved in vesicular trafficking of molecules between cellular organelles. GDIs slow the rate of dissociation of GDP from rab proteins and release GDP from membrane-bound rabs. GDI2 is ubiquitously expressed. The GDI2 gene contains many repetitive elements indicating that it may be prone to inversion/deletion rearrangements. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001494.4. 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
	GDI2	NM_001494.4	MANE Select	c.*361T>C		3_prime_UTR	Exon 11 of 11	NP_001485.2
	GDI2	NM_001115156.2		c.*361T>C		3_prime_UTR	Exon 10 of 10	NP_001108628.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GDI2	ENST00000380191.9	TSL:1 MANE Select	c.*361T>C		3_prime_UTR	Exon 11 of 11	ENSP00000369538.4
	GDI2	ENST00000380181.8	TSL:1	c.*361T>C		3_prime_UTR	Exon 10 of 10	ENSP00000369528.3
	GDI2	ENST00000865639.1		c.*361T>C		3_prime_UTR	Exon 12 of 12	ENSP00000535698.1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52496 AN: 151916 Hom.: 9380 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.360

GnomAD4 exome AF: 0.359 AC: 5999 AN: 16720 Hom.: 1203 Cov.: 0 AF XY: 0.361 AC XY: 3161 AN XY: 8760

African (AFR) AF: 0.279 AC: 158 AN: 566

American (AMR) AF: 0.301 AC: 130 AN: 432

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 219 AN: 550

East Asian (EAS) AF: 0.389 AC: 232 AN: 596

South Asian (SAS) AF: 0.274 AC: 186 AN: 678

European-Finnish (FIN) AF: 0.351 AC: 236 AN: 672

Middle Eastern (MID) AF: 0.377 AC: 40 AN: 106

European-Non Finnish (NFE) AF: 0.366 AC: 4412 AN: 12070

Other (OTH) AF: 0.368 AC: 386 AN: 1050

GnomAD4 genome AF: 0.346 AC: 52538 AN: 152036 Hom.: 9392 Cov.: 31 AF XY: 0.344 AC XY: 25537 AN XY: 74336

African (AFR) AF: 0.263 AC: 10899 AN: 41462

American (AMR) AF: 0.375 AC: 5729 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1357 AN: 3462

East Asian (EAS) AF: 0.354 AC: 1828 AN: 5168

South Asian (SAS) AF: 0.358 AC: 1725 AN: 4818

European-Finnish (FIN) AF: 0.341 AC: 3610 AN: 10580

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26196 AN: 67964

Other (OTH) AF: 0.362 AC: 764 AN: 2110

Alfa AF: 0.376 Hom.: 3701

Bravo AF: 0.343

Asia WGS AF: 0.334 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.57
PhyloP100		1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs2497; hg19: chr10-5807608;