rs2344396

Variant names:

• chr5-62309740-A-G
• rs2344396
• NM_001098511.3:c.64+3204A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-62309740-A-G
• chr5-62309740-A-T

Variant summary

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

The NM_001098511.3(KIF2A):​c.64+3204A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,920 control chromosomes in the GnomAD database, including 30,566 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 0.63 (30566 hom., cov: 31)
• Consequence: KIF2A NM_001098511.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 3 publications found

Genes affected

KIF2A (HGNC:6318): (kinesin family member 2A) The protein encoded by this gene is a plus end-directed motor required for normal mitotic progression. The encoded protein is required for normal spindle activity during mitosis and is necessary for normal brain development. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

KIF2A Gene-Disease associations (from GenCC):

• complex cortical dysplasia with other brain malformations 3

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae)

ENSG00000288643 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001098511.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF2A	NM_001098511.3	MANE Select	c.64+3204A>G		intron	N/A	NP_001091981.1
	KIF2A	NM_004520.5		c.64+3204A>G		intron	N/A	NP_004511.2
	KIF2A	NM_001243953.2		c.64+3204A>G		intron	N/A	NP_001230882.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF2A	ENST00000407818.8	TSL:1 MANE Select	c.64+3204A>G		intron	N/A	ENSP00000385000.3
	KIF2A	ENST00000401507.7	TSL:1	c.64+3204A>G		intron	N/A	ENSP00000385622.3
	KIF2A	ENST00000381103.7	TSL:1	c.-18+1229A>G		intron	N/A	ENSP00000370493.3

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96075 AN: 151802 Hom.: 30545 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.633 AC: 96143 AN: 151920 Hom.: 30566 Cov.: 31 AF XY: 0.631 AC XY: 46847 AN XY: 74258

African (AFR) AF: 0.599 AC: 24816 AN: 41398

American (AMR) AF: 0.611 AC: 9340 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2081 AN: 3468

East Asian (EAS) AF: 0.510 AC: 2638 AN: 5168

South Asian (SAS) AF: 0.684 AC: 3293 AN: 4814

European-Finnish (FIN) AF: 0.660 AC: 6950 AN: 10526

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44983 AN: 67958

Other (OTH) AF: 0.666 AC: 1404 AN: 2108

Alfa AF: 0.646 Hom.: 89272

Bravo AF: 0.623

Asia WGS AF: 0.596 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.62
PhyloP100		-0.25
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: rs2344396; hg19: chr5-61605567; COSMIC: COSV66944964; COSMIC: COSV66944964;