5-132710020-C-T

Position:

• chr5-132710020-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001300791.2(KIF3A):​c.1228+939G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,974 control chromosomes in the GnomAD database, including 10,989 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 0.32 (10989 hom., cov: 32)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• 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/exons	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.1228+939G>A		intron_variant		ENST00000403231.6	NP_001287720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF3A	ENST00000403231.6	c.1228+939G>A		intron_variant		2	NM_001300791.2	ENSP00000385808.1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48818 AN: 151856 Hom.: 10958 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.322 AC: 48907 AN: 151974 Hom.: 10989 Cov.: 32 AF XY: 0.331 AC XY: 24555 AN XY: 74256

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.262

Alfa AF: 0.117 Hom.: 201

Bravo AF: 0.337

Asia WGS AF: 0.457 AC: 1585 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	16
DANN	Benign	0.75

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: rs12514685; hg19: chr5-132045712;