5-132700560-T-C

Position:

• chr5-132700560-T-C

Variant summary

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

The NM_001300791.2(KIF3A):​c.1938+87A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 873,044 control chromosomes in the GnomAD database, including 333,713 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 0.86 (55878 hom., cov: 30)
  • Exomes 𝑓: 0.88 (277835 hom.)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.957

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]

KIF3A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.1938+87A>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.1938+87A>G		intron_variant		2	NM_001300791.2	ENSP00000385808.1

Frequencies

GnomAD3 genomes AF: 0.855 AC: 130071 AN: 152054 Hom.: 55862 Cov.: 30

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.854

GnomAD4 exome AF: 0.877 AC: 632271 AN: 720872 Hom.: 277835 Cov.: 9 AF XY: 0.875 AC XY: 335951 AN XY: 384156

Gnomad4 AFR exome AF: 0.792

Gnomad4 AMR exome AF: 0.844

Gnomad4 ASJ exome AF: 0.869

Gnomad4 EAS exome AF: 0.908

Gnomad4 SAS exome AF: 0.821

Gnomad4 FIN exome AF: 0.892

Gnomad4 NFE exome AF: 0.888

Gnomad4 OTH exome AF: 0.873

GnomAD4 genome AF: 0.855 AC: 130133 AN: 152172 Hom.: 55878 Cov.: 30 AF XY: 0.854 AC XY: 63507 AN XY: 74386

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.893

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.854

Alfa AF: 0.875 Hom.: 80756

Bravo AF: 0.849

Asia WGS AF: 0.890 AC: 3097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.80

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: rs1468216; hg19: chr5-132036252;