rs2344396

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF2A	NM_001098511.3	c.64+3204A>G		intron_variant		ENST00000407818.8
KIF2A	NM_001243952.2	c.-18+1229A>G		intron_variant
KIF2A	NM_001243953.2	c.64+3204A>G		intron_variant
KIF2A	NM_004520.5	c.64+3204A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF2A	ENST00000407818.8	c.64+3204A>G		intron_variant		1	NM_001098511.3	A1

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

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.666

Alfa AF: 0.650 Hom.: 54390

Bravo AF: 0.623

Asia WGS AF: 0.596 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.62

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

Publications

LitVar

Other links and lift over

dbSNP: rs2344396; hg19: chr5-61605567; COSMIC: COSV66944964; COSMIC: COSV66944964;