rs2299007

Positions:

• chr5-132707340-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001300791.2(KIF3A):​c.1301-881T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,134 control chromosomes in the GnomAD database, including 2,844 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 (2844 hom., cov: 31)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.68

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.1301-881T>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.1301-881T>C		intron_variant		2	NM_001300791.2	ENSP00000385808
	ENST00000628061.1	n.112-15721A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24139 AN: 152016 Hom.: 2842 Cov.: 31

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.159 AC: 24150 AN: 152134 Hom.: 2844 Cov.: 31 AF XY: 0.171 AC XY: 12727 AN XY: 74382

Gnomad4 AFR AF: 0.0668

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.140

Alfa AF: 0.142 Hom.: 1819

Bravo AF: 0.150

Asia WGS AF: 0.309 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	18
DANN	Benign	0.78

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: rs2299007; hg19: chr5-132043032;