rs17691077

chr5-132707659-A-Cchr5-132707659-A-G

Variant summary

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

The NM_001300791.2(KIF3A):c.1301-1200T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0815 in 152,210 control chromosomes in the GnomAD database, including 655 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 0.082 (655 hom., cov: 32)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF3A	NM_001300791.2	c.1301-1200T>G		intron_variant		ENST00000403231.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF3A	ENST00000403231.6	c.1301-1200T>G		intron_variant		2	NM_001300791.2
	ENST00000628061.1	n.112-15402A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12413 AN: 152092 Hom.: 655 Cov.: 32

Gnomad AFR AF: 0.0229

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.0984

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.0815 AC: 12408 AN: 152210 Hom.: 655 Cov.: 32 AF XY: 0.0787 AC XY: 5860 AN XY: 74416

Gnomad4 AFR AF: 0.0228

Gnomad4 AMR AF: 0.0983

Gnomad4 ASJ AF: 0.0956

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0512

Gnomad4 FIN AF: 0.0759

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.0965

Alfa AF: 0.0948 Hom.: 555

Bravo AF: 0.0809

Asia WGS AF: 0.0210 AC: 71 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.2
Dann	Benign	0.42

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: rs17691077; hg19: chr5-132043351;