rs9784675

Positions:

• chr5-132734047-A-G
• chr5-132734047-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001300791.2(KIF3A):​c.280+158T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,978 control chromosomes in the GnomAD database, including 11,107 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 0.33 (11107 hom., cov: 32)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.280+158T>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.280+158T>C		intron_variant		2	NM_001300791.2	ENSP00000385808

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49319 AN: 151860 Hom.: 11078 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.325 AC: 49407 AN: 151978 Hom.: 11107 Cov.: 32 AF XY: 0.334 AC XY: 24814 AN XY: 74278

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.267

Alfa AF: 0.180 Hom.: 4276

Bravo AF: 0.340

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.34

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: rs9784675; hg19: chr5-132069739;