rs2299011

Positions:

• chr5-132706850-C-G
• chr5-132706850-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001300791.2(KIF3A):​c.1301-391G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,920 control chromosomes in the GnomAD database, including 10,979 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 0.32 (10979 hom., cov: 32)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

Genes affected

KIF3A (HGNC:6319): (kinesin family member 3A) Enables protein phosphatase binding activity; small GTPase binding activity; and spectrin binding activity. Involved in protein localization to cell junction and protein transport. Located in centriole and centrosome. Part of kinesin II complex. Colocalizes with spindle microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000230612 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.1301-391G>C		intron_variant		ENST00000403231.6	NP_001287720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF3A	ENST00000403231.6	c.1301-391G>C		intron_variant		2	NM_001300791.2	ENSP00000385808.1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48783 AN: 151804 Hom.: 10949 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.322 AC: 48870 AN: 151920 Hom.: 10979 Cov.: 32 AF XY: 0.331 AC XY: 24560 AN XY: 74226

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.262

Alfa AF: 0.257 Hom.: 877

Bravo AF: 0.337

Asia WGS AF: 0.460 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	13
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs2299011; hg19: chr5-132042542;