5-132727868-A-T

Variant names:

• chr5-132727868-A-T
• rs3798129
• NM_001300791.2:c.281-1370T>A

Variant summary

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

The NM_001300791.2(KIF3A):​c.281-1370T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,042 control chromosomes in the GnomAD database, including 12,915 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 0.35 (12915 hom., cov: 32)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 5 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 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.281-1370T>A		intron	N/A	NP_001287720.1
	KIF3A	NM_001300792.2		c.281-1370T>A		intron	N/A	NP_001287721.1
	KIF3A	NM_007054.7		c.281-1370T>A		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.281-1370T>A		intron	N/A	ENSP00000385808.1
	KIF3A	ENST00000378735.5	TSL:1	c.281-1370T>A		intron	N/A	ENSP00000368009.1
	KIF3A	ENST00000618515.4	TSL:5	c.281-1370T>A		intron	N/A	ENSP00000483023.1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52535 AN: 151924 Hom.: 12878 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.346 AC: 52638 AN: 152042 Hom.: 12915 Cov.: 32 AF XY: 0.355 AC XY: 26361 AN XY: 74320

African (AFR) AF: 0.649 AC: 26888 AN: 41440

American (AMR) AF: 0.341 AC: 5211 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3466

East Asian (EAS) AF: 0.748 AC: 3865 AN: 5170

South Asian (SAS) AF: 0.185 AC: 893 AN: 4820

European-Finnish (FIN) AF: 0.363 AC: 3832 AN: 10556

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10726 AN: 67986

Other (OTH) AF: 0.285 AC: 602 AN: 2112

Alfa AF: 0.123 Hom.: 215

Bravo AF: 0.365

Asia WGS AF: 0.465 AC: 1618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.26
DANN	Benign	0.93
PhyloP100		-1.8
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: rs3798129; hg19: chr5-132063560;