rs10069772

Positions:

• chr5-132704996-A-G
• chr5-132704996-A-T

Variant summary

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

The NM_001300791.2(KIF3A):​c.1310-1377T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.908 in 151,804 control chromosomes in the GnomAD database, including 62,764 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 0.91 (62764 hom., cov: 31)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.1310-1377T>C		intron_variant		ENST00000403231.6	NP_001287720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF3A	ENST00000403231.6	c.1310-1377T>C		intron_variant		2	NM_001300791.2	ENSP00000385808
	ENST00000628061.1	n.111+15162A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.908 AC: 137711 AN: 151686 Hom.: 62710 Cov.: 31

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.908 AC: 137824 AN: 151804 Hom.: 62764 Cov.: 31 AF XY: 0.906 AC XY: 67218 AN XY: 74182

Gnomad4 AFR AF: 0.978

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.892

Alfa AF: 0.899 Hom.: 7647

Bravo AF: 0.911

Asia WGS AF: 0.905 AC: 3147 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.8
DANN	Benign	0.64

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: rs10069772; hg19: chr5-132040688;