5-132707121-G-T

Variant names:

• chr5-132707121-G-T
• rs2299009
• NM_001300791.2:c.1301-662C>A

Variant summary

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

The NM_001300791.2(KIF3A):​c.1301-662C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 150,848 control chromosomes in the GnomAD database, including 26,780 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 0.56 (26780 hom., cov: 30)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 11 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.1301-662C>A		intron_variant	Intron 10 of 18	ENST00000403231.6	NP_001287720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF3A	ENST00000403231.6	c.1301-662C>A		intron_variant	Intron 10 of 18	2	NM_001300791.2	ENSP00000385808.1

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85216 AN: 150780 Hom.: 26791 Cov.: 30

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.663

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.565 AC: 85219 AN: 150848 Hom.: 26780 Cov.: 30 AF XY: 0.555 AC XY: 40844 AN XY: 73556

African (AFR) AF: 0.330 AC: 13568 AN: 41124

American (AMR) AF: 0.548 AC: 8341 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2452 AN: 3468

East Asian (EAS) AF: 0.141 AC: 726 AN: 5140

South Asian (SAS) AF: 0.641 AC: 3072 AN: 4790

European-Finnish (FIN) AF: 0.541 AC: 5457 AN: 10084

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.728 AC: 49306 AN: 67732

Other (OTH) AF: 0.611 AC: 1280 AN: 2094

Alfa AF: 0.510 Hom.: 2190

Bravo AF: 0.546

Asia WGS AF: 0.416 AC: 1432 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		0.11
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: rs2299009; hg19: chr5-132042813;