5-132707340-A-G

Variant names:

• chr5-132707340-A-G
• rs2299007
• NM_001300791.2:c.1301-881T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000403231.6(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 ENST00000403231.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.68
• Publications: 20 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000403231.6. 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
	KIF3A	NM_001300791.2	MANE Select	c.1301-881T>C		intron	N/A	NP_001287720.1
	KIF3A	NM_001300792.2		c.1229-881T>C		intron	N/A	NP_001287721.1
	KIF3A	NM_007054.7		c.1228+3619T>C		intron	N/A	NP_008985.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF3A	ENST00000403231.6	TSL:2 MANE Select	c.1301-881T>C		intron	N/A	ENSP00000385808.1
	KIF3A	ENST00000378735.5	TSL:1	c.1229-881T>C		intron	N/A	ENSP00000368009.1
	KIF3A	ENST00000618515.4	TSL:5	c.1298-881T>C		intron	N/A	ENSP00000483023.1

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

African (AFR) AF: 0.0668 AC: 2775 AN: 41550

American (AMR) AF: 0.234 AC: 3578 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3472

East Asian (EAS) AF: 0.531 AC: 2747 AN: 5174

South Asian (SAS) AF: 0.160 AC: 771 AN: 4818

European-Finnish (FIN) AF: 0.353 AC: 3724 AN: 10560

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9820 AN: 67982

Other (OTH) AF: 0.140 AC: 296 AN: 2110

Alfa AF: 0.142 Hom.: 2281

Bravo AF: 0.150

Asia WGS AF: 0.309 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	18
DANN	Benign	0.78
PhyloP100		2.7
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: rs2299007; hg19: chr5-132043032;