Variant 1-200606666-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014875.3(KIF14):c.1607+80T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 1,233,608 control chromosomes in the GnomAD database, including 71,262 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.34 ( 8812 hom., cov: 31)

Exomes 𝑓: 0.33 ( 62450 hom. )

Consequence

KIF14
NM_014875.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.00800

Variant links:

Genes affected

KIF14 (HGNC:19181): (kinesin family member 14) This gene encodes a member of the kinesin-3 superfamily of microtubule motor proteins. These proteins are involved in numerous processes including vesicle transport, chromosome segregation, mitotic spindle formation, and cytokinesis. In human HeLa-S3 and 293T cells, this protein is localized to the cytoplasm during interphase, to the spindle poles and spindle microtubules during mitosis, and to the midbody during cytokinesis. An internal motor domain displays microtubule-dependent ATPase activity, consistent with its function as a microtubule motor protein. Knockdown of this gene results in failed cytokinesis with endoreplication, which results in multinucleated cells. This gene has been identified as a likely oncogene in breast, lung and ovarian cancers, as well as retinoblastomas and gliomas. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2015]

KIF14 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 1-200606666-A-G is Benign according to our data. Variant chr1-200606666-A-G is described in ClinVar as [Benign]. Clinvar id is 1226287.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF14	NM_014875.3 linkuse as main transcript	c.1607+80T>C		intron_variant		ENST00000367350.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF14	ENST00000367350.5 linkuse as main transcript	c.1607+80T>C		intron_variant		2	NM_014875.3	P1
KIF14	ENST00000614960.4 linkuse as main transcript	c.1607+80T>C		intron_variant		1		P1

Frequencies

GnomAD3 genomes

AF:

0.336

AC:

50993

AN:

151860

Hom.:

8807

Cov.:

show subpopulations

Gnomad AFR

AF:

0.354

Gnomad AMI

AF:

0.374

Gnomad AMR

AF:

0.303

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.165

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.443

Gnomad MID

AF:

0.309

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.291

GnomAD4 exome

AF:

0.334

AC:

360768

AN:

1081630

Hom.:

62450

AF XY:

0.330

AC XY:

183282

AN XY:

554850

show subpopulations

Gnomad4 AFR exome

AF:

0.348

Gnomad4 AMR exome

AF:

0.300

Gnomad4 ASJ exome

AF:

0.247

Gnomad4 EAS exome

AF:

0.155

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.451

Gnomad4 NFE exome

AF:

0.348

Gnomad4 OTH exome

AF:

0.322

GnomAD4 genome

AF:

0.336

AC:

51027

AN:

151978

Hom.:

8812

Cov.:

AF XY:

0.335

AC XY:

24920

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.354

Gnomad4 AMR

AF:

0.304

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.165

Gnomad4 SAS

AF:

0.247

Gnomad4 FIN

AF:

0.443

Gnomad4 NFE

AF:

0.341

Gnomad4 OTH

AF:

0.289

Alfa

AF:

0.332

Hom.:

13701

Bravo

AF:

0.327

Asia WGS

AF:

0.206

AC:

719

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

DANN

Benign

0.75

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over