rs41289846

chr20-32334328-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_004798.4(KIF3B):c.*3009G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 152,666 control chromosomes in the GnomAD database, including 115 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 0.030 (112 hom., cov: 32)
  • Exomes 𝑓: 0.076 (3 hom.)
• Consequence: KIF3B NM_004798.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

KIF3B (HGNC:6320): (kinesin family member 3B) The protein encoded by this gene acts as a heterodimer with kinesin family member 3A to aid in chromosome movement during mitosis and meiosis. The encoded protein is a plus end-directed microtubule motor and can interact with the SMC3 subunit of the cohesin complex. In addition, the encoded protein may be involved in the intracellular movement of membranous organelles. This protein and kinesin family member 3A form the kinesin II subfamily of the kinesin superfamily. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0304 (4623/152150) while in subpopulation NFE AF= 0.045 (3063/68016). AF 95% confidence interval is 0.0437. There are 112 homozygotes in gnomad4. There are 2309 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 113 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF3B	NM_004798.4	c.*3009G>A		3_prime_UTR_variant	9/9	ENST00000375712.4
KIF3B	XM_047440589.1	c.*3009G>A		3_prime_UTR_variant	9/9
KIF3B	XM_047440590.1	c.*3009G>A		3_prime_UTR_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF3B	ENST00000375712.4	c.*3009G>A		3_prime_UTR_variant	9/9	1	NM_004798.4	P1

Frequencies

GnomAD3 genomes AF: 0.0304 AC: 4627 AN: 152032 Hom.: 113 Cov.: 32

Gnomad AFR AF: 0.00727

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0183

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00663

Gnomad FIN AF: 0.0803

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0450

Gnomad OTH AF: 0.0201

GnomAD4 exome AF: 0.0756 AC: 39 AN: 516 Hom.: 3 Cov.: 0 AF XY: 0.0693 AC XY: 23 AN XY: 332

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.0829

Gnomad4 NFE exome AF: 0.0500

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0304 AC: 4623 AN: 152150 Hom.: 112 Cov.: 32 AF XY: 0.0310 AC XY: 2309 AN XY: 74368

Gnomad4 AFR AF: 0.00725

Gnomad4 AMR AF: 0.0181

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00663

Gnomad4 FIN AF: 0.0803

Gnomad4 NFE AF: 0.0450

Gnomad4 OTH AF: 0.0199

Alfa AF: 0.0375 Hom.: 31

Bravo AF: 0.0245

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.17
Dann	Benign	0.59

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: rs41289846; hg19: chr20-30922131;