chr20-32277706-CCCG-C

Position:

• chr20-32277706-CCCG-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_004798.4(KIF3B):​c.-89_-87delGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0146 in 246,740 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency:
  • Genomes: 𝑓 0.0018 (0 hom., cov: 31)
  • Exomes 𝑓: 0.035 (0 hom.)
• Consequence: KIF3B NM_004798.4 5_prime_UTR
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 0.00

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 -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF3B	NM_004798.4	c.-89_-87delGCC		5_prime_UTR_variant	1/9	ENST00000375712.4	NP_004789.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF3B	ENST00000375712	c.-89_-87delGCC		5_prime_UTR_variant	1/9	1	NM_004798.4	ENSP00000364864.3

Frequencies

GnomAD3 genomes AF: 0.00181 AC: 273 AN: 150644 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000657

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.00119

Gnomad ASJ AF: 0.00405

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.00209

Gnomad FIN AF: 0.00234

Gnomad MID AF: 0.00323

Gnomad NFE AF: 0.00252

Gnomad OTH AF: 0.00242

GnomAD4 exome AF: 0.0347 AC: 3334 AN: 96004 Hom.: 0 AF XY: 0.0363 AC XY: 1987 AN XY: 54752

Gnomad4 AFR exome AF: 0.0272

Gnomad4 AMR exome AF: 0.0248

Gnomad4 ASJ exome AF: 0.0334

Gnomad4 EAS exome AF: 0.0259

Gnomad4 SAS exome AF: 0.0569

Gnomad4 FIN exome AF: 0.0307

Gnomad4 NFE exome AF: 0.0358

Gnomad4 OTH exome AF: 0.0345

GnomAD4 genome AF: 0.00182 AC: 274 AN: 150736 Hom.: 0 Cov.: 31 AF XY: 0.00190 AC XY: 140 AN XY: 73626

Gnomad4 AFR AF: 0.000679

Gnomad4 AMR AF: 0.00119

Gnomad4 ASJ AF: 0.00405

Gnomad4 EAS AF: 0.000196

Gnomad4 SAS AF: 0.00209

Gnomad4 FIN AF: 0.00234

Gnomad4 NFE AF: 0.00252

Gnomad4 OTH AF: 0.00240

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Retinal dystrophy Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg

Jan 01, 2022

- -

Computational scores

Source: dbNSFP v4.3

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: rs756318630; hg19: chr20-30865509;