5-132711097-G-C

Position:

• chr5-132711097-G-C

Variant summary

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

The NM_001300791.2(KIF3A):​c.1130-40C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 1,576,946 control chromosomes in the GnomAD database, including 389,390 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 (28553 hom., cov: 30)
  • Exomes 𝑓: 0.70 (360837 hom.)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.1130-40C>G		intron_variant		ENST00000403231.6	NP_001287720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF3A	ENST00000403231.6	c.1130-40C>G		intron_variant		2	NM_001300791.2	ENSP00000385808
	ENST00000628061.1	n.112-11964G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89521 AN: 151708 Hom.: 28553 Cov.: 30

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.637

GnomAD3 exomes AF: 0.601 AC: 150116 AN: 249878 Hom.: 49669 AF XY: 0.620 AC XY: 83749 AN XY: 135070

Gnomad AFR exome AF: 0.392

Gnomad AMR exome AF: 0.412

Gnomad ASJ exome AF: 0.725

Gnomad EAS exome AF: 0.141

Gnomad SAS exome AF: 0.668

Gnomad FIN exome AF: 0.545

Gnomad NFE exome AF: 0.740

Gnomad OTH exome AF: 0.662

GnomAD4 exome AF: 0.699 AC: 996747 AN: 1425122 Hom.: 360837 Cov.: 25 AF XY: 0.701 AC XY: 498444 AN XY: 711106

Gnomad4 AFR exome AF: 0.394

Gnomad4 AMR exome AF: 0.429

Gnomad4 ASJ exome AF: 0.722

Gnomad4 EAS exome AF: 0.183

Gnomad4 SAS exome AF: 0.666

Gnomad4 FIN exome AF: 0.552

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.671

GnomAD4 genome AF: 0.590 AC: 89548 AN: 151824 Hom.: 28553 Cov.: 30 AF XY: 0.579 AC XY: 42950 AN XY: 74192

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.634

Alfa AF: 0.663 Hom.: 6170

Bravo AF: 0.577

Asia WGS AF: 0.449 AC: 1563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.3
DANN	Benign	0.49

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: rs11740584; hg19: chr5-132046789; COSMIC: COSV66413680;