chr5-132713424-T-C

Variant names:

• chr5-132713424-T-C
• rs1080001
• NM_001300791.2:c.1129+2333A>G

Variant summary

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

The NM_001300791.2(KIF3A):​c.1129+2333A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,060 control chromosomes in the GnomAD database, including 7,002 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 0.27 (7002 hom., cov: 32)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.1129+2333A>G		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.1129+2333A>G		intron_variant	Intron 8 of 18	2	NM_001300791.2	ENSP00000385808.1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40336 AN: 151942 Hom.: 7000 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.266 AC: 40373 AN: 152060 Hom.: 7002 Cov.: 32 AF XY: 0.275 AC XY: 20436 AN XY: 74288

African (AFR) AF: 0.388 AC: 16082 AN: 41468

American (AMR) AF: 0.299 AC: 4566 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 522 AN: 3470

East Asian (EAS) AF: 0.753 AC: 3891 AN: 5164

South Asian (SAS) AF: 0.181 AC: 874 AN: 4820

European-Finnish (FIN) AF: 0.356 AC: 3756 AN: 10540

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10162 AN: 68008

Other (OTH) AF: 0.221 AC: 468 AN: 2114

Alfa AF: 0.230 Hom.: 643

Bravo AF: 0.272

Asia WGS AF: 0.440 AC: 1531 AN: 3478

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	0.59
PhyloP100		0.76
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: rs1080001; hg19: chr5-132049116;