16-57843736-C-T

Variant names:

• chr16-57843736-C-T
• rs247041
• ENST00000563028.1:c.108+18993G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
KIFC3	XM_006721188.2	c.108+18993G>A		intron_variant	Intron 1 of 21		XP_006721251.1
KIFC3	XM_005255937.2	c.108+18993G>A		intron_variant	Intron 1 of 20		XP_005255994.1
KIFC3	XM_017023221.2	c.108+18993G>A		intron_variant	Intron 1 of 21		XP_016878710.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIFC3	ENST00000563028.1	c.108+18993G>A		intron_variant	Intron 1 of 2	4		ENSP00000456354.1
KIFC3	ENST00000565684.5	c.-40+2613G>A		intron_variant	Intron 1 of 4	5		ENSP00000455276.1

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

African (AFR) AF: 0.196 AC: 8141 AN: 41470

American (AMR) AF: 0.478 AC: 7296 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3472

East Asian (EAS) AF: 0.620 AC: 3204 AN: 5164

South Asian (SAS) AF: 0.388 AC: 1873 AN: 4826

European-Finnish (FIN) AF: 0.493 AC: 5191 AN: 10540

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.575 AC: 39084 AN: 67956

Other (OTH) AF: 0.489 AC: 1031 AN: 2110

Alfa AF: 0.538 Hom.: 87048

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs247041; hg19: chr16-57877640;