chr20-32277706-C-CCCG

Position:

• chr20-32277706-C-CCCG

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The NM_004798.4(KIF3B):​c.-89_-87dupGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.024 in 261,104 control chromosomes in the GnomAD database, including 105 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.031 (96 hom., cov: 31)
  • Exomes 𝑓: 0.014 (9 hom.)
• Consequence: KIF3B NM_004798.4 5_prime_UTR
• Clinical Significance: Likely benign no assertion criteria provided B: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 -9 ACMG points.

• BP6: Variant 20-32277706-C-CCCG is Benign according to our data. Variant chr20-32277706-C-CCCG is described in ClinVar as [Likely_benign]. Clinvar id is 3250120.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0553 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0311 AC: 4682 AN: 150708 Hom.: 95 Cov.: 31

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.00983

Gnomad EAS AF: 0.0173

Gnomad SAS AF: 0.0140

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.0226

Gnomad NFE AF: 0.0196

Gnomad OTH AF: 0.0261

GnomAD4 exome AF: 0.0143 AC: 1574 AN: 110302 Hom.: 9 Cov.: 0 AF XY: 0.0140 AC XY: 901 AN XY: 64578

Gnomad4 AFR exome AF: 0.0429

Gnomad4 AMR exome AF: 0.0242

Gnomad4 ASJ exome AF: 0.00697

Gnomad4 EAS exome AF: 0.0103

Gnomad4 SAS exome AF: 0.00703

Gnomad4 FIN exome AF: 0.00711

Gnomad4 NFE exome AF: 0.0150

Gnomad4 OTH exome AF: 0.0165

GnomAD4 genome AF: 0.0311 AC: 4689 AN: 150802 Hom.: 96 Cov.: 31 AF XY: 0.0306 AC XY: 2255 AN XY: 73674

Gnomad4 AFR AF: 0.0572

Gnomad4 AMR AF: 0.0424

Gnomad4 ASJ AF: 0.00983

Gnomad4 EAS AF: 0.0176

Gnomad4 SAS AF: 0.0142

Gnomad4 FIN AF: 0.0111

Gnomad4 NFE AF: 0.0196

Gnomad4 OTH AF: 0.0264

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Optic atrophy Benign:1

Likely benign, no assertion criteria provided

clinical testing

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

Jan 01, 2023

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Computational scores

Source: dbNSFP v4.3

Splicing

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;