16-57843736-C-T

Variant summary

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

The ENST00000563028.1(KIFC3):c.108+18993G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,002 control chromosomes in the GnomAD database, including 17,692 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 0.45 (17692 hom., cov: 31)
• Consequence: KIFC3 ENST00000563028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

Genes affected

KIFC3 (HGNC:6326): (kinesin family member C3) This gene encodes a member of the kinesin-14 family of microtubule motors. Members of this family play a role in the formation, maintenance and remodeling of the bipolar mitotic spindle. The protein encoded by this gene has cytoplasmic functions in the interphase cells. It may also be involved in the final stages of cytokinesis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIFC3	XM_005255937.2	c.108+18993G>A		intron_variant
KIFC3	XM_006721188.2	c.108+18993G>A		intron_variant
KIFC3	XM_011523075.2	c.108+18993G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIFC3	ENST00000563028.1	c.108+18993G>A		intron_variant		4
KIFC3	ENST00000565684.5	c.-40+2613G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68536 AN: 151884 Hom.: 17691 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.451 AC: 68554 AN: 152002 Hom.: 17692 Cov.: 31 AF XY: 0.446 AC XY: 33101 AN XY: 74268

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.489

Alfa AF: 0.555 Hom.: 40413

Bravo AF: 0.444

Asia WGS AF: 0.453 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.6
Dann	Benign	0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs247041; hg19: chr16-57877640;