5-132704682-T-A

Variant names:

• chr5-132704682-T-A
• rs10062446
• NM_001300791.2:c.1310-1063A>T

Variant summary

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

The NM_001300791.2(KIF3A):​c.1310-1063A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,638 control chromosomes in the GnomAD database, including 28,480 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 0.59 (28480 hom., cov: 31)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 10 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=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF3A	NM_001300791.2	MANE Select	c.1310-1063A>T		intron	N/A	NP_001287720.1
	KIF3A	NM_001300792.2		c.1238-1063A>T		intron	N/A	NP_001287721.1
	KIF3A	NM_007054.7		c.1229-1063A>T		intron	N/A	NP_008985.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF3A	ENST00000403231.6	TSL:2 MANE Select	c.1310-1063A>T		intron	N/A	ENSP00000385808.1
	KIF3A	ENST00000378735.5	TSL:1	c.1238-1063A>T		intron	N/A	ENSP00000368009.1
	KIF3A	ENST00000618515.4	TSL:5	c.1307-1063A>T		intron	N/A	ENSP00000483023.1

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89301 AN: 151518 Hom.: 28480 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.589 AC: 89327 AN: 151638 Hom.: 28480 Cov.: 31 AF XY: 0.578 AC XY: 42837 AN XY: 74118

African (AFR) AF: 0.399 AC: 16542 AN: 41418

American (AMR) AF: 0.562 AC: 8564 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2471 AN: 3462

East Asian (EAS) AF: 0.166 AC: 857 AN: 5168

South Asian (SAS) AF: 0.648 AC: 3118 AN: 4812

European-Finnish (FIN) AF: 0.536 AC: 5661 AN: 10552

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49754 AN: 67674

Other (OTH) AF: 0.633 AC: 1331 AN: 2102

Alfa AF: 0.645 Hom.: 4086

Bravo AF: 0.577

Asia WGS AF: 0.448 AC: 1558 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.8
DANN	Benign	0.70
PhyloP100		-0.11
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: rs10062446; hg19: chr5-132040374; COSMIC: COSV66413665; COSMIC: COSV66413665;