5-76631363-C-T

Variant names:

• chr5-76631363-C-T
• rs410262
• NM_006633.5:c.1613-496C>T

Variant summary

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

The NM_006633.5(IQGAP2):​c.1613-496C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,960 control chromosomes in the GnomAD database, including 24,868 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 0.57 (24868 hom., cov: 32)
• Consequence: IQGAP2 NM_006633.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 2 publications found

Genes affected

IQGAP2 (HGNC:6111): (IQ motif containing GTPase activating protein 2) This gene encodes a member of the IQGAP family. The encoded protein contains three IQ domains, one calponin homology domain, one Ras-GAP domain and one WW domain. This protein interacts with components of the cytoskeleton, with cell adhesion molecules, and with several signaling molecules to regulate cell morphology and motility. It also acts as a tumor suppressor and has been found to play a role in regulating innate antiviral responses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2017]

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 (SAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006633.5. 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
	IQGAP2	NM_006633.5	MANE Select	c.1613-496C>T		intron	N/A	NP_006624.3
	IQGAP2	NM_001285460.2		c.1463-496C>T		intron	N/A	NP_001272389.2
	IQGAP2	NM_001285461.2		c.272-496C>T		intron	N/A	NP_001272390.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IQGAP2	ENST00000274364.11	TSL:1 MANE Select	c.1613-496C>T		intron	N/A	ENSP00000274364.6
	IQGAP2	ENST00000396234.7	TSL:1	c.272-496C>T		intron	N/A	ENSP00000379535.3
	IQGAP2	ENST00000514350.5	TSL:1	c.1532-496C>T		intron	N/A	ENSP00000423672.1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86765 AN: 151840 Hom.: 24857 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.571 AC: 86812 AN: 151960 Hom.: 24868 Cov.: 32 AF XY: 0.571 AC XY: 42400 AN XY: 74272

African (AFR) AF: 0.555 AC: 22972 AN: 41426

American (AMR) AF: 0.527 AC: 8043 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2190 AN: 3466

East Asian (EAS) AF: 0.463 AC: 2396 AN: 5172

South Asian (SAS) AF: 0.632 AC: 3043 AN: 4816

European-Finnish (FIN) AF: 0.558 AC: 5889 AN: 10562

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40370 AN: 67942

Other (OTH) AF: 0.591 AC: 1247 AN: 2110

Alfa AF: 0.589 Hom.: 13404

Bravo AF: 0.566

Asia WGS AF: 0.510 AC: 1779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		0.47
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: rs410262; hg19: chr5-75927188; COSMIC: COSV57175101; COSMIC: COSV57175101;