5-132705744-C-T

Variant names:

• chr5-132705744-C-T
• rs3798132
• NM_001300791.2:c.1309+707G>A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.1309+707G>A		intron_variant	Intron 11 of 18	ENST00000403231.6	NP_001287720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF3A	ENST00000403231.6	c.1309+707G>A		intron_variant	Intron 11 of 18	2	NM_001300791.2	ENSP00000385808.1

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

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.320

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.77
DANN	Benign	0.55

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: rs3798132; hg19: chr5-132041436;