Variant 1-200553157-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_014875.3(KIF14):c.*231G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 286,084 control chromosomes in the GnomAD database, including 2,509 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.13 ( 1435 hom., cov: 32)

Exomes 𝑓: 0.12 ( 1074 hom. )

Consequence

KIF14
NM_014875.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.75

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.04).

BP6

Variant 1-200553157-C-T is Benign according to our data. Variant chr1-200553157-C-T is described in ClinVar as [Benign]. Clinvar id is 1265811.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 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.*231G>A		3_prime_UTR_variant	30/30	ENST00000367350.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF14	ENST00000367350.5 linkuse as main transcript	c.*231G>A		3_prime_UTR_variant	30/30	2	NM_014875.3	P1
KIF14	ENST00000614960.4 linkuse as main transcript	c.*231G>A		3_prime_UTR_variant	29/29	1		P1

Frequencies

GnomAD3 genomes

AF:

0.127

AC:

19328

AN:

151772

Hom.:

1434

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.0615

Gnomad AMR

AF:

0.0919

Gnomad ASJ

AF:

0.0643

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.0153

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.105

GnomAD4 exome

AF:

0.115

AC:

15452

AN:

134194

Hom.:

1074

Cov.:

AF XY:

0.114

AC XY:

7960

AN XY:

69934

show subpopulations

Gnomad4 AFR exome

AF:

0.139

Gnomad4 AMR exome

AF:

0.0728

Gnomad4 ASJ exome

AF:

0.0669

Gnomad4 EAS exome

AF:

0.000106

Gnomad4 SAS exome

AF:

0.0201

Gnomad4 FIN exome

AF:

0.188

Gnomad4 NFE exome

AF:

0.131

Gnomad4 OTH exome

AF:

0.111

GnomAD4 genome

AF:

0.127

AC:

19333

AN:

151890

Hom.:

1435

Cov.:

AF XY:

0.126

AC XY:

9354

AN XY:

74212

show subpopulations

Gnomad4 AFR

AF:

0.146

Gnomad4 AMR

AF:

0.0919

Gnomad4 ASJ

AF:

0.0643

Gnomad4 EAS

AF:

0.000388

Gnomad4 SAS

AF:

0.0156

Gnomad4 FIN

AF:

0.200

Gnomad4 NFE

AF:

0.135

Gnomad4 OTH

AF:

0.105

Alfa

AF:

0.0746

Hom.:

Bravo

AF:

0.119

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

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

-1.0

CADD

Benign

0.70

DANN

Benign

0.46

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