NM_001300791.2:c.1309+707G>A

Variant names:

• chr5-132705744-C-T
• rs3798132
• NM_001300791.2:c.1309+707G>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.1309+707G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,828 control chromosomes in the GnomAD database, including 18,440 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 0.40 (18440 hom., cov: 32)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993
• Publications: 5 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001300791.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF3A	NM_001300791.2	MANE Select	c.1309+707G>A		intron	N/A	NP_001287720.1	E9PES4
	KIF3A	NM_001300792.2		c.1237+707G>A		intron	N/A	NP_001287721.1	J3KPF9
	KIF3A	NM_007054.7		c.1229-2125G>A		intron	N/A	NP_008985.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF3A	ENST00000403231.6	TSL:2 MANE Select	c.1309+707G>A		intron	N/A	ENSP00000385808.1	E9PES4
	KIF3A	ENST00000378735.5	TSL:1	c.1237+707G>A		intron	N/A	ENSP00000368009.1	J3KPF9
	KIF3A	ENST00000618515.4	TSL:5	c.1306+707G>A		intron	N/A	ENSP00000483023.1	A0A087X011

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60095 AN: 151710 Hom.: 18388 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.397 AC: 60210 AN: 151828 Hom.: 18440 Cov.: 32 AF XY: 0.402 AC XY: 29867 AN XY: 74218

African (AFR) AF: 0.821 AC: 34038 AN: 41472

American (AMR) AF: 0.361 AC: 5516 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 560 AN: 3462

East Asian (EAS) AF: 0.755 AC: 3907 AN: 5178

South Asian (SAS) AF: 0.184 AC: 890 AN: 4824

European-Finnish (FIN) AF: 0.362 AC: 3820 AN: 10544

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10735 AN: 67772

Other (OTH) AF: 0.320 AC: 673 AN: 2104

Alfa AF: 0.128 Hom.: 238

Bravo AF: 0.423

Asia WGS AF: 0.473 AC: 1636 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.77
DANN	Benign	0.55
PhyloP100		-0.99
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: rs3798132; hg19: chr5-132041436;