rs10520686

Variant names:

• chr15-90454197-C-G
• rs10520686
• NM_003870.4:c.1488-231C>G

Your query was ambiguous. Multiple possible variants found:

• chr15-90454197-C-G
• chr15-90454197-C-T

Variant summary

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

The NM_003870.4(IQGAP1):​c.1488-231C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,130 control chromosomes in the GnomAD database, including 2,797 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 0.16 (2797 hom., cov: 32)
• Consequence: IQGAP1 NM_003870.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 5 publications found

Genes affected

IQGAP1 (HGNC:6110): (IQ motif containing GTPase activating protein 1) This gene encodes a member of the IQGAP family. The protein contains four IQ domains, one calponin homology domain, one Ras-GAP domain and one WW domain. It interacts with components of the cytoskeleton, with cell adhesion molecules, and with several signaling molecules to regulate cell morphology and motility. Expression of the protein is upregulated by gene amplification in two gastric cancer cell lines. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IQGAP1	NM_003870.4	c.1488-231C>G		intron_variant	Intron 13 of 37	ENST00000268182.10	NP_003861.1
IQGAP1	XM_047433204.1	c.1488-231C>G		intron_variant	Intron 13 of 29		XP_047289160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IQGAP1	ENST00000268182.10	c.1488-231C>G		intron_variant	Intron 13 of 37	1	NM_003870.4	ENSP00000268182.5
IQGAP1	ENST00000560738.1	c.107-11850C>G		intron_variant	Intron 2 of 24	5		ENSP00000453181.1
IQGAP1	ENST00000633485.1	n.1488-231C>G		intron_variant	Intron 13 of 38	5		ENSP00000488618.1

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24695 AN: 152012 Hom.: 2779 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.163 AC: 24730 AN: 152130 Hom.: 2797 Cov.: 32 AF XY: 0.169 AC XY: 12595 AN XY: 74388

African (AFR) AF: 0.119 AC: 4920 AN: 41494

American (AMR) AF: 0.326 AC: 4974 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2502 AN: 5180

South Asian (SAS) AF: 0.293 AC: 1411 AN: 4814

European-Finnish (FIN) AF: 0.143 AC: 1517 AN: 10576

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8585 AN: 68006

Other (OTH) AF: 0.166 AC: 349 AN: 2108

Alfa AF: 0.0532 Hom.: 55

Bravo AF: 0.177

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.62
PhyloP100		-0.076
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: rs10520686; hg19: chr15-90997429;