10-32019466-A-C

Position:

• chr10-32019466-A-C

Variant summary

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

The NM_004521.3(KIF5B):​c.2306+392T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0886 in 152,250 control chromosomes in the GnomAD database, including 1,113 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 0.089 (1113 hom., cov: 33)
• Consequence: KIF5B NM_004521.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366

Genes affected

KIF5B (HGNC:6324): (kinesin family member 5B) Enables identical protein binding activity; microtubule binding activity; and microtubule motor activity. Involved in several processes, including lysosome localization; natural killer cell mediated cytotoxicity; and positive regulation of protein localization to plasma membrane. Located in centriolar satellite; cytosol; and vesicle. [provided by Alliance of Genome Resources, Apr 2022]

LOC107984219 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF5B	NM_004521.3	c.2306+392T>G		intron_variant		ENST00000302418.5	NP_004512.1
LOC107984219	XR_001747415.2	n.6794A>C		non_coding_transcript_exon_variant	3/3
KIF5B	XM_047425202.1	c.2306+392T>G		intron_variant			XP_047281158.1
KIF5B	XM_047425203.1	c.2024+392T>G		intron_variant			XP_047281159.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF5B	ENST00000302418.5	c.2306+392T>G		intron_variant		1	NM_004521.3	ENSP00000307078	P1
KIF5B	ENST00000493889.1	n.175+392T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0887 AC: 13496 AN: 152132 Hom.: 1116 Cov.: 33

Gnomad AFR AF: 0.0190

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0851

Gnomad OTH AF: 0.0890

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

GnomAD4 genome AF: 0.0886 AC: 13484 AN: 152250 Hom.: 1113 Cov.: 33 AF XY: 0.0961 AC XY: 7150 AN XY: 74432

Gnomad4 AFR AF: 0.0189

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0853

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.0851

Gnomad4 OTH AF: 0.0890

Alfa AF: 0.0854 Hom.: 840

Bravo AF: 0.0837

Asia WGS AF: 0.247 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.9
DANN	Benign	0.78

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: rs2286746; hg19: chr10-32308394;