rs1775715

Positions:

• chr10-32020077-A-G

Variant summary

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

The NM_004521.3(KIF5B):​c.2205-118T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 670,524 control chromosomes in the GnomAD database, including 90,036 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 0.47 (17735 hom., cov: 32)
  • Exomes 𝑓: 0.53 (72301 hom.)
• Consequence: KIF5B NM_004521.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF5B	NM_004521.3	c.2205-118T>C		intron_variant		ENST00000302418.5	NP_004512.1
KIF5B	XM_047425202.1	c.2205-118T>C		intron_variant			XP_047281158.1
KIF5B	XM_047425203.1	c.1923-118T>C		intron_variant			XP_047281159.1
LOC107984219	XR_001747415.2	n.7405A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF5B	ENST00000302418.5	c.2205-118T>C		intron_variant		1	NM_004521.3	ENSP00000307078.4
KIF5B	ENST00000493889.1	n.74-118T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72059 AN: 151834 Hom.: 17733 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.480

GnomAD4 exome AF: 0.527 AC: 273497 AN: 518572 Hom.: 72301 AF XY: 0.526 AC XY: 145805 AN XY: 276950

Gnomad4 AFR exome AF: 0.362

Gnomad4 AMR exome AF: 0.514

Gnomad4 ASJ exome AF: 0.507

Gnomad4 EAS exome AF: 0.650

Gnomad4 SAS exome AF: 0.508

Gnomad4 FIN exome AF: 0.616

Gnomad4 NFE exome AF: 0.518

Gnomad4 OTH exome AF: 0.521

GnomAD4 genome AF: 0.474 AC: 72085 AN: 151952 Hom.: 17735 Cov.: 32 AF XY: 0.479 AC XY: 35600 AN XY: 74246

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.478

Alfa AF: 0.505 Hom.: 32597

Bravo AF: 0.460

Asia WGS AF: 0.516 AC: 1792 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.38
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1775715; hg19: chr10-32309005;