5-132713335-C-T

Variant names:

• chr5-132713335-C-T
• rs2897442
• NM_001300791.2:c.1130-2278G>A

Variant summary

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

The NM_001300791.2(KIF3A):​c.1130-2278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,994 control chromosomes in the GnomAD database, including 25,024 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 0.51 (25024 hom., cov: 31)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.1130-2278G>A		intron_variant	Intron 8 of 18	ENST00000403231.6	NP_001287720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF3A	ENST00000403231.6	c.1130-2278G>A		intron_variant	Intron 8 of 18	2	NM_001300791.2	ENSP00000385808.1

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78234 AN: 151876 Hom.: 25029 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.515 AC: 78235 AN: 151994 Hom.: 25024 Cov.: 31 AF XY: 0.507 AC XY: 37639 AN XY: 74284

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.575

Alfa AF: 0.668 Hom.: 11083

Bravo AF: 0.491

Asia WGS AF: 0.435 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.63
DANN	Benign	0.40

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: rs2897442; hg19: chr5-132049027; COSMIC: COSV66413700;